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Lee SQE, Ma GL, Candra H, Khandelwal S, Pang LM, Low ZJ, Cheang QW, Liang ZX. Streptomyces sungeiensis SD3 as a Microbial Chassis for the Heterologous Production of Secondary Metabolites. ACS Synth Biol 2024; 13:1259-1272. [PMID: 38513222 DOI: 10.1021/acssynbio.3c00750] [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] [Indexed: 03/23/2024]
Abstract
We present the newly isolated Streptomyces sungeiensis SD3 strain as a promising microbial chassis for heterologous production of secondary metabolites. S. sungeiensis SD3 exhibits several advantageous traits as a microbial chassis, including genetic tractability, rapid growth, susceptibility to antibiotics, and metabolic capability supporting secondary metabolism. Genomic and transcriptomic sequencing unveiled the primary metabolic capabilities and secondary biosynthetic pathways of S. sungeiensis SD3, including a previously unknown pathway responsible for the biosynthesis of streptazone B1. The unique placement of S. sungeiensis SD3 in the phylogenetic tree designates it as a type strain, setting it apart from other frequently employed Streptomyces chassis. This distinction makes it the preferred chassis for expressing biosynthetic gene clusters (BGCs) derived from strains within the same phylogenetic or neighboring phylogenetic clade. The successful expression of secondary biosynthetic pathways from a closely related yet slow-growing strain underscores the utility of S. sungeiensis SD3 as a heterologous expression chassis. Validation of CRISPR/Cas9-assisted genetic tools for chromosomal deletion and insertion paved the way for further strain improvement and BGC refactoring through rational genome editing. The addition of S. sungeiensis SD3 to the heterologous chassis toolkit will facilitate the discovery and production of secondary metabolites.
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Affiliation(s)
- Sean Qiu En Lee
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Srashti Khandelwal
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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2
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Mou Q, Han T, Tian M, Liu M. Light-Driven Photocatalyst-Free Synthesis of β, δ-Functionalized Ketones from Aldehydes. J Org Chem 2024; 89:5189-5199. [PMID: 38511413 DOI: 10.1021/acs.joc.4c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The synthesis of ketones has been a long focus of chemistry research, on account of its unique reactivity. Herein, we report a simple light-driven photocatalyst-free synthesis of β, δ-functionalized ketones from aldehydes, using inexpensive and commercially abundant feedstock chemicals. This reaction is enabled by the direct acyl radical generation via hydrogen atom transfer and the subsequent radical addition process, avoiding the need for prefunctionalized substrates and organometallic reagent.
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Affiliation(s)
- Quansheng Mou
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Tongyu Han
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Miao Tian
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Mingxin Liu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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3
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Das B, Chakraborty N, Dhara HN, Bhattacharyya P, Patel BK. Access to Chromenopyrrole via Tandem [3 + 2] Cycloaddition and Intramolecular C-O Coupling. J Org Chem 2024. [PMID: 38171005 DOI: 10.1021/acs.joc.3c02479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
A mild and concise method for the synthesis of chromenopyrrole from 2'-hydroxychalcone is devised. The reaction proceeds via an initial [3 + 2] cycloaddition on the C═C bond of 2'-hydroxychalcone and 1,3-dipolarophile, generated in situ by the reaction of ethyl isocyanoacetate and AgOAc. This is then followed by an intramolecular C-O bond formation with the -OH group and C5-H of the in situ generated pyrrole, leading to chromenopyrroles.
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Affiliation(s)
- Bubul Das
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039, India
- Department of Chemistry, Bagadhar Brahma Kishan College, Jalah, Assam 781327, India
| | - Nikita Chakraborty
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039, India
| | - Hirendra Nath Dhara
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039, India
| | - Pratip Bhattacharyya
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039, India
| | - Bhisma K Patel
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039, India
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Tanoeyadi S, Tsunoda T, Ito T, Philmus B, Mahmud T. Acarbose May Function as a Competitive Exclusion Agent for the Producing Bacteria. ACS Chem Biol 2023; 18:367-376. [PMID: 36648321 PMCID: PMC9957957 DOI: 10.1021/acschembio.2c00795] [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: 01/18/2023]
Abstract
Acarbose is a well-known microbial specialized metabolite used clinically to treat type 2 diabetes. This natural pseudo-oligosaccharide (PsOS) shows potent inhibitory activity toward various glycosyl hydrolases, including α-glucosidases and α-amylases. While acarbose and other PsOSs are produced by many different bacteria, their ecological or biological role in microbial communities is still an open question. Here, we show that several PsOS-producing actinobacteria, i.e., Actinoplanes sp. SE50/110 (acarbose producer), Streptomyces glaucescens GLA.O (acarbose producer), and Streptomyces dimorphogenes ATCC 31484 (trestatin producer), can grow in the presence of acarbose, while the growth of the non-PsOS-producing organism Streptomyces coelicolor M1152 was suppressed when starch is the main source of energy. Further investigations using recombinant α-amylases from S. coelicolor M1152 and the PsOS-producing actinobacteria revealed that the S. coelicolor α-amylase was inhibited by acarbose, whereas those from the PsOS-producing bacteria were not inhibited by acarbose. Bioinformatic and protein modeling studies suggested that a point mutation in the α-amylases of the PsOS-producing actinobacteria is responsible for the resistance of those enzymes toward acarbose. Converting the acarbose-resistant α-amylase AcbE to its A304H variant diminished its acarbose-resistance property. Taken together, the results suggest that acarbose is used by the producing bacteria as a competitive exclusion agent to suppress the growth of other microorganisms in their natural environment, while the producing organisms equip themselves with α-amylase variants that are resistant to acarbose.
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Affiliation(s)
- Samuel Tanoeyadi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Takuya Ito
- Laboratory of Natural Medicines, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nisikiorikita, Tondabayashi 584-8540 (Japan)
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
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5
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Louwen JJR, Kautsar SA, van der Burg S, Medema MH, van der Hooft JJJ. iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures. PLoS Comput Biol 2023; 19:e1010462. [PMID: 36758069 PMCID: PMC9946207 DOI: 10.1371/journal.pcbi.1010462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/22/2023] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Microbial specialised metabolism is full of valuable natural products that are applied clinically, agriculturally, and industrially. The genes that encode their biosynthesis are often physically clustered on the genome in biosynthetic gene clusters (BGCs). Many BGCs consist of multiple groups of co-evolving genes called sub-clusters that are responsible for the biosynthesis of a specific chemical moiety in a natural product. Sub-clusters therefore provide an important link between the structures of a natural product and its BGC, which can be leveraged for predicting natural product structures from sequence, as well as for linking chemical structures and metabolomics-derived mass features to BGCs. While some initial computational methodologies have been devised for sub-cluster detection, current approaches are not scalable, have only been run on small and outdated datasets, or produce an impractically large number of possible sub-clusters to mine through. Here, we constructed a scalable method for unsupervised sub-cluster detection, called iPRESTO, based on topic modelling and statistical analysis of co-occurrence patterns of enzyme-coding protein families. iPRESTO was used to mine sub-clusters across 150,000 prokaryotic BGCs from antiSMASH-DB. After annotating a fraction of the resulting sub-cluster families, we could predict a substructure for 16% of the antiSMASH-DB BGCs. Additionally, our method was able to confirm 83% of the experimentally characterised sub-clusters in MIBiG reference BGCs. Based on iPRESTO-detected sub-clusters, we could correctly identify the BGCs for xenorhabdin and salbostatin biosynthesis (which had not yet been annotated in BGC databases), as well as propose a candidate BGC for akashin biosynthesis. Additionally, we show for a collection of 145 actinobacteria how substructures can aid in linking BGCs to molecules by correlating iPRESTO-detected sub-clusters to MS/MS-derived Mass2Motifs substructure patterns. This work paves the way for deeper functional and structural annotation of microbial BGCs by improved linking of orphan molecules to their cognate gene clusters, thus facilitating accelerated natural product discovery.
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Affiliation(s)
- Joris J. R. Louwen
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Satria A. Kautsar
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | | | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
- * E-mail: (MHM); (JJJvdH)
| | - Justin J. J. van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- * E-mail: (MHM); (JJJvdH)
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6
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Tsunoda T, Asamizu S, Mahmud T. Biochemical Characterization of GacI, a Bifunctional Glycosyltransferase-Phosphatase Enzyme Involved in Acarbose Biosynthesis in Streptomyces glaucescens GLA.O. Biochemistry 2022; 61:2628-2635. [PMID: 36288494 PMCID: PMC9669214 DOI: 10.1021/acs.biochem.2c00473] [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: 11/29/2022]
Abstract
Acarbose, a pseudotetrasaccharide produced by several strains of Actinoplanes and Streptomyces, is an α-glucosidase inhibitor clinically used to control type II diabetes. Bioinformatic analysis of the biosynthetic gene clusters of acarbose in Actinoplanes sp. SE50/110 (the acb cluster) and Streptomyces glaucescens GLA.O (the gac cluster) revealed their distinct genetic organizations and presumably biosynthetic pathways. However, to date, only the acarbose pathway in the SE50/110 strain has been extensively studied. Here, we report that GacI, one of the proteins that appear to be different between the two pathways, is a bifunctional glycosyltransferase family 5 (GT5)-phosphatase (PP) enzyme that functions at two different steps in acarbose biosynthesis in S. glaucescens GLA.O. In the acb pathway, the GT and the PP reactions are performed by two different enzymes. Truncated GacI proteins having only the GT or the PP domain showed comparable catalytic activity with the full-length GacI, indicating that domain separation does not significantly affect their respective catalytic activity. GacI, which is widely distributed in many Streptomyces, represents the first example of naturally occurring GT5-PP bifunctional enzymes biochemically characterized.
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Affiliation(s)
- Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Shumpei Asamizu
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
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7
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Yi D, Niroula D, Gutekunst WR, Loper JE, Yan Q, Agarwal V. A Nonfunctional Halogenase Masquerades as an Aromatizing Dehydratase in Biosynthesis of Pyrrolic Polyketides by Type I Polyketide Synthases. ACS Chem Biol 2022; 17:1351-1356. [PMID: 35675261 DOI: 10.1021/acschembio.2c00288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial modular type I polyketide synthases (PKSs) typically furnish nonaromatic lactone and lactam natural products. Here, by the complete in vitro enzymatic production of the polyketide antibiotic pyoluteorin, we describe the biosynthetic mechanism for the construction of an aromatic resorcylic ring by a type I PKS. We find that the pyoluteorin type I PKS does not produce an aromatic product, rather furnishing an alicyclic dihydrophloroglucinol that is later enzymatically dehydrated and aromatized. The aromatizing dehydratase is encoded in the pyoluteorin biosynthetic gene cluster (BGC), and its presence is conserved in other BGCs encoding production of pyrrolic polyketides. Sequence similarity and mutational analysis demonstrates that the overall structure and position of the active site for the aromatizing dehydratase is shared with flavin-dependent halogenases albeit with a loss in ability to perform redox catalysis. We demonstrate that the post-PKS dehydrative aromatization is critical for the antibiotic activity of pyoluteorin.
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Affiliation(s)
- Dongqi Yi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dhirendra Niroula
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Will R Gutekunst
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, United States.,USDA-Agricultural Research Service, Corvallis, Oregon 97330, United States
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717, United States.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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8
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Tsunoda T, Samadi A, Burade S, Mahmud T. Complete biosynthetic pathway to the antidiabetic drug acarbose. Nat Commun 2022; 13:3455. [PMID: 35705566 PMCID: PMC9200736 DOI: 10.1038/s41467-022-31232-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/30/2022] [Indexed: 11/11/2022] Open
Abstract
Acarbose is a bacterial-derived α-glucosidase inhibitor clinically used to treat patients with type 2 diabetes. As type 2 diabetes is on the rise worldwide, the market demand for acarbose has also increased. Despite its significant therapeutic importance, how it is made in nature is not completely understood. Here, we report the complete biosynthetic pathway to acarbose and its structural components, GDP-valienol and O-4-amino-(4,6-dideoxy-α-D-glucopyranosyl)-(1→4)-O-α-D-glucopyranosyl-(1→4)-D-glucopyranose. GDP-valienol is derived from valienol 7-phosphate, catalyzed by three cyclitol modifying enzymes, whereas O-4-amino-(4,6-dideoxy-α-D-glucopyranosyl)-(1→4)-O-α-D-glucopyranosyl-(1→4)-D-glucopyranose is produced from dTDP-4-amino-4,6-dideoxy-D-glucose and maltose by the glycosyltransferase AcbI. The final assembly process is catalyzed by a pseudoglycosyltransferase enzyme, AcbS, which is a homologue of AcbI but catalyzes the formation of a non-glycosidic C-N bond. This study clarifies all previously unknown steps in acarbose biosynthesis and establishes a complete pathway to this high value pharmaceutical. The market demand for acarbose, a drug used for treatment of patients affected by type-2 diabetes, has increased. In this article, the authors report the acarbose complete biosynthetic pathway, clarifying previously unknown steps and identifying a pseudoglycosyltransferase enzyme, AcbS, a homologue of AcbI that catalyzes the formation of a non-glycosidic C-N bond.
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Affiliation(s)
- Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331-3507, USA
| | - Arash Samadi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331-3507, USA
| | - Sachin Burade
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331-3507, USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331-3507, USA.
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10
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Yi D, Acharya A, Gumbart JC, Gutekunst WR, Agarwal V. Gatekeeping Ketosynthases Dictate Initiation of Assembly Line Biosynthesis of Pyrrolic Polyketides. J Am Chem Soc 2021; 143:7617-7622. [DOI: 10.1021/jacs.1c02371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dongqi Yi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Atanu Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C. Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Will R. Gutekunst
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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11
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Purdy TN, Kim MC, Cullum R, Fenical W, Moore BS. Discovery and Biosynthesis of Tetrachlorizine Reveals Enzymatic Benzylic Dehydrogenation via an ortho-Quinone Methide. J Am Chem Soc 2021; 143:3682-3686. [PMID: 33656337 DOI: 10.1021/jacs.0c12415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ortho-quinone methides (o-QMs) are reactive intermediates in biosynthesis that give rise to a variety of intra- and intermolecular cyclization/addition products in bacteria, fungi, and plants. Herein, we report a new metabolic deviation of an o-QM intermediate in a benzylic dehydrogenation reaction that links the newly described marine bacterial natural products dihydrotetrachlorizine and tetrachlorizine. We discovered these novel dichloropyrrole-containing compounds from actinomycete strain AJS-327 that unexpectedly harbors in its genome a biosynthetic gene cluster (BGC) of striking similarity to that of chlorizidine, another marine alkaloid bearing a different carbon skeleton. Heterologous expression of the homologous flavin-dependent oxidoreductase enzymes Tcz9 and Clz9 revealed their native functions in tetrachlorizine and chlorizidine biosynthesis, respectively, supporting divergent oxidative dehydrogenation and pyrrolizine-forming reactions. Swapping these berberine bridge enzyme-like oxidoreductases, we produced cyclized and dehydrogenated analogs of tetrachlorizine and chlorizidine, including a dearomatized chlorizidine analog that stabilizes an o-QM via conjugation with a 3H-pyrrolizine ring.
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12
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Zhou W, Posri P, Mahmud T. Natural Occurrence of Hybrid Polyketides from Two Distinct Biosynthetic Pathways in Streptomyces pactum. ACS Chem Biol 2021; 16:270-276. [PMID: 33601889 DOI: 10.1021/acschembio.0c00982] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nature has always been seemingly limitless in its ability to create new chemical entities. It provides vastly diverse natural compounds through a biomanufacturing process that involves myriads of biosynthetic machineries. Here we report a case of unusual formations of hybrid natural products that are derived from two distinct polyketide biosynthetic pathways, the NFAT-133 and conglobatin pathways, in Streptomyces pactum ATCC 27456. Their chemical structures were determined by NMR spectroscopy, mass spectrometry, and chemical synthesis. Genome sequence analysis and gene inactivation experiments uncovered the biosynthetic gene cluster of conglobatin in S. pactum. Biochemical studies of the recombinant thioesterase (TE) domain of the conglobatin polyketide synthase (PKS) as well as its S74A mutant revealed that the formation of these hybrid compounds requires an active TE domain. We propose that NFAT-133 can interfere with conglobatin biosynthesis by reacting with the TE-domain-bound intermediates in the conglobatin PKS assembly line to form hybrid NFAT-133/conglobatin products.
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Affiliation(s)
- Wei Zhou
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, United States
| | - Priyapan Posri
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, United States
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, United States
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13
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Jaremko MJ, Davis TD, Corpuz JC, Burkart MD. Type II non-ribosomal peptide synthetase proteins: structure, mechanism, and protein-protein interactions. Nat Prod Rep 2020; 37:355-379. [PMID: 31593192 PMCID: PMC7101270 DOI: 10.1039/c9np00047j] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: 1990 to 2019 Many medicinally-relevant compounds are derived from non-ribosomal peptide synthetase (NRPS) products. Type I NRPSs are organized into large modular complexes, while type II NRPS systems contain standalone or minimal domains that often encompass specialized tailoring enzymes that produce bioactive metabolites. Protein-protein interactions and communication between the type II biosynthetic machinery and various downstream pathways are critical for efficient metabolite production. Importantly, the architecture of type II NRPS proteins makes them ideal targets for combinatorial biosynthesis and metabolic engineering. Future investigations exploring the molecular basis or protein-protein recognition in type II NRPS pathways will guide these engineering efforts. In this review, we consolidate the broad range of NRPS systems containing type II proteins and focus on structural investigations, enzymatic mechanisms, and protein-protein interactions important to unraveling pathways that produce unique metabolites, including dehydrogenated prolines, substituted benzoic acids, substituted amino acids, and cyclopropanes.
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Affiliation(s)
- Matt J Jaremko
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Joshua C Corpuz
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
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14
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A severe leakage of intermediates to shunt products in acarbose biosynthesis. Nat Commun 2020; 11:1468. [PMID: 32193369 PMCID: PMC7081202 DOI: 10.1038/s41467-020-15234-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 02/23/2020] [Indexed: 11/08/2022] Open
Abstract
The α-glucosidase inhibitor acarbose, produced by Actinoplanes sp. SE50/110, is a well-known drug for the treatment of type 2 diabetes mellitus. However, the largely unexplored biosynthetic mechanism of this compound has impeded further titer improvement. Herein, we uncover that 1-epi-valienol and valienol, accumulated in the fermentation broth at a strikingly high molar ratio to acarbose, are shunt products that are not directly involved in acarbose biosynthesis. Additionally, we find that inefficient biosynthesis of the amino-deoxyhexose moiety plays a role in the formation of these shunt products. Therefore, strategies to minimize the flux to the shunt products and to maximize the supply of the amino-deoxyhexose moiety are implemented, which increase the acarbose titer by 1.2-fold to 7.4 g L−1. This work provides insights into the biosynthesis of the C7-cyclitol moiety and highlights the importance of assessing shunt product accumulation when seeking to improve the titer of microbial pharmaceutical products. Biosynthetic mechanism for the type 2 diabetes treatment drug acarbose is not fully revealed. Here, the authors show that shunt pathways and inefficient amino-deoxyhexose biosynthesis lead to 1-epi-valienol and valienol accumulation, and minimizing the flux to these shunt products can increase acarbose titer in Actinoplanes species.
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15
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Li B, Kuang Y, He JB, Tang R, Xu LL, Leung CH, Ma DL, Qiao X, Ye M. Antcamphorols A-K, Cytotoxic and ROS Scavenging Triterpenoids from Antrodia camphorata. JOURNAL OF NATURAL PRODUCTS 2020; 82:318-323. [PMID: 31891260 DOI: 10.1021/acs.jnatprod.8b00753] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Antrodia camphorata is a rare and valuable medicinal mushroom. In this work, 11 new triterpenoids, namely, antcamphorols A-K (1-11), together with 10 known triterpenoids, 12-21, were isolated from dish-cultured A. camphorata. Compound 1 is an unprecedented C31 lanostane-type triterpenoid featuring a methyl group at C-15 and a C-21-O-C-24 tetrahydropyran ring at C-17. Compounds 2-11 are ergostane-type triterpenoids, and they include two pairs of norergostanes 2-5. The structures of the new compounds were identified by NMR, 2D NMR, and HRESIMS data analyses. The absolute configurations of 1 and 6 were defined by X-ray diffraction data, and the absolute configuration at C-25 of 4 was determined by the modified Mosher's method. Compounds 7, 9, 10, 16, and 19 showed significant ROS scavenging activities (63.9-70.5% at 20 μM) in high-glucose-induced HUVECs. Compounds 3 and 8 exhibited moderate cytotoxic activities against U251 (IC50, 9.2 μM) and MCF-7 (IC50, 8.1 μM) human cancer cell lines, respectively.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Natural and Biomimetic Drugs & Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Beijing 100191 , People's Republic of China
| | - Yi Kuang
- State Key Laboratory of Natural and Biomimetic Drugs & Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Beijing 100191 , People's Republic of China
| | - Jun-Bin He
- State Key Laboratory of Natural and Biomimetic Drugs & Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Beijing 100191 , People's Republic of China
| | - Rui Tang
- State Key Laboratory of Natural and Biomimetic Drugs & Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Beijing 100191 , People's Republic of China
| | - Lu-Lu Xu
- State Key Laboratory of Natural and Biomimetic Drugs & Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Beijing 100191 , People's Republic of China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences , University of Macau , Macau , People's Republic of China
| | - Dik-Lung Ma
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong SWT 802 , Hong Kong , People's Republic of China
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs & Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Beijing 100191 , People's Republic of China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs & Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Beijing 100191 , People's Republic of China
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16
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Tata S, Aouiche A, Bijani C, Bouras N, Pont F, Mathieu F, Sabaou N. Mzabimycins A and B, novel intracellular angucycline antibiotics produced by Streptomyces sp. PAL114 in synthetic medium containing L-tryptophan. Saudi Pharm J 2019; 27:907-913. [PMID: 31997896 PMCID: PMC6978613 DOI: 10.1016/j.jsps.2019.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 06/12/2019] [Indexed: 01/09/2023] Open
Abstract
In our previous studies, the production of four bioactive molecules by Streptomyces sp. PAL114 in complex ISP2 broth medium has been described. Three of these molecules belong to the angucycline family. In this study, two novel antibiotics belonging to the same family were produced by strain PAL114 on M2 synthetic medium containing L-tryptophan as precursor. These antibiotics, named mzabimycins A and B, were intracellular and produced only in the presence of L-tryptophan. After four days of culturing PAL114 in the M2 medium, the bioactive compounds were extracted from mycelium with methanol and then analyzed by HPLC on reverse phase C18 column. Two active purplish blue fractions were purified. The chemical structures of these molecules were determined on the basis of spectroscopic and spectrometric analyses (1H and 13C NMR, and mass spectra). They were identified to be novel angucycline derivative antibiotics. The pure molecules showed activity against some pathogenic Gram-positive bacteria which have multiple antibiotic resistance, such as Staphylococcus aureus MRSA 639c and Listeria monocytogenes ATCC 13932.
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Affiliation(s)
- Samira Tata
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Alger, Algeria
| | - Adel Aouiche
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Alger, Algeria
| | - Christian Bijani
- Laboratoire de Chimie de Coordination (LCC), CNRS, Université de Toulouse, UPS, INPT, LCC, 205 Route de Narbonne, 31077 Toulouse, France
| | - Noureddine Bouras
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Alger, Algeria
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaïa, BP 455, Ghardaïa 47000, Algeria
| | - Frédéric Pont
- Proteomics Group, Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM UMR1037, Toulouse, France
| | - Florence Mathieu
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, Toulouse, France
| | - Nasserdine Sabaou
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Alger, Algeria
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17
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Niehs SP, Dose B, Scherlach K, Pidot SJ, Stinear TP, Hertweck C. Genome Mining Reveals Endopyrroles from a Nonribosomal Peptide Assembly Line Triggered in Fungal-Bacterial Symbiosis. ACS Chem Biol 2019; 14:1811-1818. [PMID: 31283172 DOI: 10.1021/acschembio.9b00406] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial endosymbiont (Burkholderia rhizoxinica) of the rice seedling blight fungus (Rhizopus microsporus) harbors a large number of cryptic biosynthesis gene clusters. Genome mining and sequence similarity networks based on an encoded nonribosomal peptide assembly line and the associated pyrrole-forming enzymes in the symbiont indicated that the encoded metabolites are unique among a large number of tentative pyrrole natural products in diverse and unrelated bacterial phyla. By performing comparative metabolic profiling using a mutant generated with an improved pheS Burkholderia counterselection marker, we found that the symbionts' biosynthetic pathway is mainly activated under salt stress and exclusively in symbiosis with the fungal host. The cryptic metabolites were fully characterized as novel pyrrole-substituted depsipeptides (endopyrroles). A broader survey showed that endopyrrole production is a hallmark of geographically distant endofungal bacteria, which produce the peptides solely under symbiotic conditions.
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Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne 3000, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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18
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Fu C, Xie F, Hoffmann J, Wang Q, Bauer A, Brönstrup M, Mahmud T, Müller R. Armeniaspirol Antibiotic Biosynthesis: Chlorination and Oxidative Dechlorination Steps Affording Spiro[4.4]non‐8‐ene. Chembiochem 2019; 20:764-769. [DOI: 10.1002/cbic.201800791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Chengzhang Fu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Feng Xie
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Judith Hoffmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Qiushui Wang
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Armin Bauer
- Sanofi–Aventis (Deutschland) GmbH Industriepark Höchst 65926 Frankfurt Germany
| | - Mark Brönstrup
- Helmholtz Centre for Infection Research (HZI) Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Taifo Mahmud
- Department of Pharmaceutical SciencesOregon State University Corvallis OR 97331-3507 USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI) and Department of PharmacySaarland University Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF)Partner site Hannover–Braunschweig Braunschweig Germany
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19
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Supong K, Sripreechasak P, Phongsopitanun W, Tanasupawat S, Danwisetkanjana K, Bunbamrung N, Pittayakhajonwut P. Antimicrobial substances from the rare actinomycete Nonomuraea rhodomycinica NR4-ASC07 T. Nat Prod Res 2018; 33:2285-2291. [PMID: 29451019 DOI: 10.1080/14786419.2018.1440223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nonomuraea rhodomycinica NR4-ASC07T is a rare actinomycete isolated from soil in Sirindhorn peat swamp forest. The crude extract of its culture broth exhibited antimicrobial and anticancer against diverse human pathogens and cancer cells. The chemical investigation of the crude extract led to the isolation of two new metabolites named nonomuric acid (1) and 3-hydroxy deoxydaunorubicinol aglycone (2), along with two known bioactive compounds [ε-rhodomycinone (3) and 7-deoxy-13-dihydrocarminomycinone (4)]. Compounds 1 and 3 showed antimalarial activity with the half maximal inhibitory concentration (IC50) of 8.00 and 8.88 μg mL-1, respectively. Compound 4 inhibited growth of Mycobacterium tuberculosis and Bacillus cereus at the minimum inhibitory concentrations of 50.0 and 12.50 μg mL-1, respectively. Every compound exhibited cytotoxicity against cancer cells tested at IC50 ≥ 6.34 μg mL-1. These finding are the first report of bioactive metabolites produced by strain NR4-ASC07T, suggesting that rare actinomycetes are yet promising sources for novel drug discovery.
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Affiliation(s)
- Khomsan Supong
- a Faculty of Agro-Industrial Technology, Department of Applied Science and Biotechnology , Rajamangala University of Technology Tawan-ok , Chanthaburi , Thailand.,b Faculty of Pharmaceutical Sciences, Department of Biochemistry and Microbiology , Chulalongkorn University , Bangkok , Thailand
| | - Paranee Sripreechasak
- c Faculty of Science, Department of Biotechnology , Burapha University , Chonburi , Thailand
| | | | - Somboon Tanasupawat
- b Faculty of Pharmaceutical Sciences, Department of Biochemistry and Microbiology , Chulalongkorn University , Bangkok , Thailand
| | - Kannawat Danwisetkanjana
- e National Center for Genetic Engineering and Biotechnology (BIOTEC-NSTDA) , Pathum Thani , Thailand
| | - Nantiya Bunbamrung
- e National Center for Genetic Engineering and Biotechnology (BIOTEC-NSTDA) , Pathum Thani , Thailand
| | - Pattama Pittayakhajonwut
- e National Center for Genetic Engineering and Biotechnology (BIOTEC-NSTDA) , Pathum Thani , Thailand
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20
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Wang ZP, He Y, Shao PL. Transition-metal-free synthesis of polysubstituted pyrrole derivatives via cyclization of methyl isocyanoacetate with aurone analogues. Org Biomol Chem 2018; 16:5422-5426. [DOI: 10.1039/c8ob01558a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A transition-metal-free, operationally simple and atom-economic protocol that converts isocyanoacetates and aurones to 2,3,4-trisubstituted pyrroles catalyzed by NaOH was presented.
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Affiliation(s)
- Zhi-Peng Wang
- School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Product Synthesis and Drug Research
- Chongqing University
- Chongqing 401331
- People's Republic of China
| | - Yun He
- School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Product Synthesis and Drug Research
- Chongqing University
- Chongqing 401331
- People's Republic of China
| | - Pan-Lin Shao
- School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Product Synthesis and Drug Research
- Chongqing University
- Chongqing 401331
- People's Republic of China
- College of Innovation and Entrepreneurship
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21
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Liu Y, Yi X, Luo X, Xi C. MeOTf-Mediated Annulation of Alkylnitriles and Arylalkynes Leading to Polysubstituted NH-Pyrroles. J Org Chem 2017; 82:11391-11398. [DOI: 10.1021/acs.joc.7b01845] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu Liu
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiangli Yi
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xuewei Luo
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Chanjuan Xi
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
- State
Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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22
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Osborn AR, Kean KM, Karplus PA, Mahmud T. The sedoheptulose 7-phosphate cyclases and their emerging roles in biology and ecology. Nat Prod Rep 2017; 34:945-956. [PMID: 28497152 DOI: 10.1039/c7np00017k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering up to: 1999-2016This highlight covers a family of enzymes of growing importance, the sedoheptulose 7-phosphate cyclases, initially of interest due to their involvement in the biosynthesis of pharmaceutically relevant secondary metabolites. More recently, these enzymes have been found throughout Prokarya and Eukarya, suggesting their broad potential biological roles in nature.
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Affiliation(s)
- Andrew R Osborn
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, USA.
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23
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Guérard-Hélaine C, De Sousa Lopes Moreira M, Touisni N, Hecquet L, Lemaire M, Hélaine V. Transketolase-Aldolase Symbiosis for the Stereoselective Preparation of Aldoses and Ketoses of Biological Interest. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christine Guérard-Hélaine
- Université Clermont Auvergne; CNRS; SIGMA Clermont; Institut de Chimie de Clermont-Ferrand, F-63000; Clermont-Ferrand BP 80026, F- 63171 Aubière France
| | - Maxime De Sousa Lopes Moreira
- Université Clermont Auvergne; CNRS; SIGMA Clermont; Institut de Chimie de Clermont-Ferrand, F-63000; Clermont-Ferrand BP 80026, F- 63171 Aubière France
| | - Nadia Touisni
- Université Clermont Auvergne; CNRS; SIGMA Clermont; Institut de Chimie de Clermont-Ferrand, F-63000; Clermont-Ferrand BP 80026, F- 63171 Aubière France
| | - Laurence Hecquet
- Université Clermont Auvergne; CNRS; SIGMA Clermont; Institut de Chimie de Clermont-Ferrand, F-63000; Clermont-Ferrand BP 80026, F- 63171 Aubière France
| | - Marielle Lemaire
- Université Clermont Auvergne; CNRS; SIGMA Clermont; Institut de Chimie de Clermont-Ferrand, F-63000; Clermont-Ferrand BP 80026, F- 63171 Aubière France
| | - Virgil Hélaine
- Université Clermont Auvergne; CNRS; SIGMA Clermont; Institut de Chimie de Clermont-Ferrand, F-63000; Clermont-Ferrand BP 80026, F- 63171 Aubière France
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24
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Asamizu S. Biosynthesis of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles, from actinomycetes. Biosci Biotechnol Biochem 2017; 81:871-881. [DOI: 10.1080/09168451.2017.1281726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
Actinomycetes are a major source of bioactive natural products with important pharmaceutical properties. Understanding the natural enzymatic assembly of complex small molecules is important for rational metabolic pathway design to produce “artificial” natural products in bacterial cells. This review will highlight current research on the biosynthetic mechanisms of two classes of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles. Validamycin A is a member of C7N aminocyclitol natural products from Streptomyces hygroscopicus. Here, two important biosynthetic steps, pseudoglycosyltranferase-catalyzed C–N bond formation, and C7-sugar phosphate cyclase-catalyzed divergent carbasugar formation, will be reviewed. In addition, the bis-indolic natural products indolocarbazole, staurosporine from Streptomyces sp. TP-A0274, and rearranged bis-indole violacein from Chromobacterium violaceum are reviewed including the oxidative course of the assembly pathway for the bis-indolic scaffold. The identified biosynthesis mechanisms will be useful to generating new biocatalytic tools and bioactive compounds.
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Affiliation(s)
- Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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25
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Osborn AR, Kean KM, Alseud KM, Almabruk KH, Asamizu S, Lee JA, Karplus PA, Mahmud T. Evolution and Distribution of C 7-Cyclitol Synthases in Prokaryotes and Eukaryotes. ACS Chem Biol 2017; 12:979-988. [PMID: 28182402 DOI: 10.1021/acschembio.7b00066] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Epi-5-epi-valiolone synthase (EEVS), a C7-sugar phosphate cyclase (SPC) homologous to 3-dehydroquinate synthase (DHQS), was discovered during studies of the biosynthesis of the C7N-aminocyclitol family of natural products. EEVS was originally thought to be present only in certain actinomycetes, but analyses of genome sequences showed that it is broadly distributed in both prokaryotes and eukaryotes, including vertebrates. Another SPC, desmethyl-4-deoxygadusol synthase (DDGS), was later discovered as being involved in the biosynthesis of mycosporine-like amino acid sunscreen compounds. Current database annotations are quite unreliable, with many EEVSs reported as DHQS, and most DDGSs reported as EEVS, DHQS, or simply hypothetical proteins. Here, we identify sequence features useful for distinguishing these enzymes, report a crystal structure of a representative DDGS showing the high similarity of the EEVS and DDGS enzymes, identify notable active site differences, and demonstrate the importance of two of these active site residues for catalysis by point mutations. Further, we functionally characterized two representatives of a distinct clade equidistant from known EEVS and known DDGS groups and show them to be authentic EEVSs. Moreover, we document and discuss the distribution of genes that encode EEVS and DDGS in various prokaryotes and eukaryotes, including pathogenic bacteria, plant symbionts, nitrogen-fixing bacteria, myxobacteria, cyanobacteria, fungi, stramenopiles, and animals, suggesting their broad potential biological roles in nature.
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Affiliation(s)
- Andrew R. Osborn
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, United States
| | - Kelsey M. Kean
- Department
of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-3507, United States
| | - Khaled M. Alseud
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, United States
| | - Khaled H. Almabruk
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, United States
| | - Shumpei Asamizu
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, United States
| | - Janet A. Lee
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-3507, United States
| | - Taifo Mahmud
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331-3507, United States
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26
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Saravana Kumar P, Stalin A, Lakshmi sundaram R, Duraipandiyan V, Al-Dhabi NA, Yuvaraj P, Balakrishna K, Ignacimuthu S. Isolation of chemical constituents from Nonomuraea species: In vitro and in silico evaluation of its antibacterial properties. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2017. [DOI: 10.1016/j.bjbas.2016.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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27
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Reddy CR, Panda SA, Ramaraju A. Oxidative Aza-Annulation of Enynyl Azides to 2-Keto/Formyl-1H-pyrroles. J Org Chem 2017; 82:944-949. [DOI: 10.1021/acs.joc.6b02468] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Chada Raji Reddy
- Division
of Natural Products Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500607, India
- Academy
of Scientific
and Innovative Research, New Delhi, India
| | - Sujatarani A. Panda
- Division
of Natural Products Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500607, India
- Academy
of Scientific
and Innovative Research, New Delhi, India
| | - Andhavaram Ramaraju
- Division
of Natural Products Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500607, India
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28
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Abstract
The first synthesis of carbasugars, compounds in which the ring oxygen of a monosaccharide had been replaced by a methylene moiety, was described in 1966 by Professor G. E. McCasland’s group. Seven years later, the first true natural carbasugar (5a-carba-R-D-galactopyranose) was isolated from a fermentation broth of Streptomyces sp. MA-4145. In the following decades, the chemistry and biology of carbasugars have been extensively studied. Most of these compounds show interesting biological properties, especially enzymatic inhibitory activities, and, in consequence, an important number of analogues have also been prepared in the search for improved biological activities. The aim of this review is to give coverage on the progress made in two important aspects of these compounds: the elucidation of their biosynthesis and the consideration of their biological properties, including the extensively studied carbapyranoses as well as the much less studied carbafuranoses.
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29
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Wang H, Sivonen K, Fewer DP. Genomic insights into the distribution, genetic diversity and evolution of polyketide synthases and nonribosomal peptide synthetases. Curr Opin Genet Dev 2015; 35:79-85. [PMID: 26605685 DOI: 10.1016/j.gde.2015.10.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/20/2015] [Accepted: 10/21/2015] [Indexed: 11/18/2022]
Abstract
Polyketides and nonribosomal peptides are important secondary metabolites that exhibit enormous structural diversity, have many pharmaceutical applications, and include a number of clinically important drugs. These complex metabolites are most commonly synthesized on enzymatic assembly lines of polyketide synthases and nonribosomal peptide synthetases. Genome-mining studies making use of the recent explosion in the number of genome sequences have demonstrated unexpected enzymatic diversity and greatly expanded the known distribution of these enzyme systems across the three domains of life. The wealth of data now available suggests that genome-mining efforts will uncover new natural products, novel biosynthetic mechanisms, and shed light on the origin and evolution of these important enzymes.
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Affiliation(s)
- Hao Wang
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland.
| | - Kaarina Sivonen
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
| | - David P Fewer
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
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30
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Elshahawi SI, Shaaban KA, Kharel MK, Thorson JS. A comprehensive review of glycosylated bacterial natural products. Chem Soc Rev 2015; 44:7591-697. [PMID: 25735878 PMCID: PMC4560691 DOI: 10.1039/c4cs00426d] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A systematic analysis of all naturally-occurring glycosylated bacterial secondary metabolites reported in the scientific literature up through early 2013 is presented. This comprehensive analysis of 15 940 bacterial natural products revealed 3426 glycosides containing 344 distinct appended carbohydrates and highlights a range of unique opportunities for future biosynthetic study and glycodiversification efforts.
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Affiliation(s)
- Sherif I Elshahawi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Khaled A Shaaban
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Madan K Kharel
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
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31
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Abuelizz HA, Mahmud T. Distinct Substrate Specificity and Catalytic Activity of the Pseudoglycosyltransferase VldE. ACTA ACUST UNITED AC 2015; 22:724-33. [PMID: 26051218 DOI: 10.1016/j.chembiol.2015.04.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 04/26/2015] [Accepted: 04/29/2015] [Indexed: 10/23/2022]
Abstract
The pseudoglycosyltransferase (PsGT) VldE is a glycosyltransferase-like protein that is similar to trehalose 6-phosphate synthase (OtsA). However, in contrast to OtsA, which catalyzes condensation between UDP-glucose and glucose 6-phosphate, VldE couples two pseudosugars to give a product with an α,α-N-pseudoglycosidic linkage. Despite their unique catalytic activity and important role in the biosynthesis of natural products, little is known about the molecular basis governing their substrate specificity and catalysis. Here, we report comparative biochemical and kinetic studies using recombinant OtsA, VldE, and their chimeric proteins with a variety of sugar and pseudosugar substrates. We found that the chimeric enzymes can produce hybrid pseudo-(amino)disaccharides, and an amino group in the acceptor is necessary to facilitate a coupling reaction with a pseudosugar donor. Furthermore, we found that the N-terminal domains of the enzymes not only play a major role in selecting the acceptors, but also control the type of nucleotidyl diphosphate moiety of the donors.
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Affiliation(s)
- Hatem A Abuelizz
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, USA.
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Liang DM, Liu JH, Wu H, Wang BB, Zhu HJ, Qiao JJ. Glycosyltransferases: mechanisms and applications in natural product development. Chem Soc Rev 2015; 44:8350-74. [DOI: 10.1039/c5cs00600g] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation reactions mainly catalyzed by glycosyltransferases (Gts) occur almost everywhere in the biosphere, and always play crucial roles in vital processes.
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Affiliation(s)
- Dong-Mei Liang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jia-Heng Liu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hao Wu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Bin-Bin Wang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hong-Ji Zhu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jian-Jun Qiao
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
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Arul Jose P, Sivakala KK, Rajeswari P, Jebakumar SRD. Characterization of antibiotic producing rare actinomycete Nonomuraea sp. JAJ18 derived from an Indian coastal solar saltern. ScientificWorldJournal 2014; 2014:456070. [PMID: 25587565 PMCID: PMC4281464 DOI: 10.1155/2014/456070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/10/2014] [Accepted: 11/28/2014] [Indexed: 11/30/2022] Open
Abstract
Rare actinomycete genera are accepted as a promising source of novel metabolites having pharmaceutical importance. One such genus of rare actinomycete is Nonomuraea. The present study was aimed at characterizing the antibiotic producing Nonomuraea strain JAJ18 which was previously isolated from coastal solar saltern. Strain JAJ18 was recognized as a member of genus Nonomuraea based on its almost complete 16S rRNA gene sequence and phenotypic characteristics. The strain JAJ18 was found to be closely related to Nonomuraea maheshkhaliensis 16-5-14(T) (98.90%), Nonomuraea candida HMC10(T) (98.58%), and Nonomuraea jabiensis A4036(T) (98.43%). From cell-free culture broth of strain JAJ18, an antibiotic was extracted and purified by silica column chromatography. The obtained antibiotic was found to be active against a range of Gram-positive and Gram-negative bacteria including drug-resistant Staphylococcus, with minimal inhibitory concentration (MIC) ranging from 0.5 to 16.0 µg mL(-1). The structural characteristics of antibiotic were determined by FTIR and NMR spectroscopy. The antibiotic was identified to be an aliphatic rich compound with significant dissimilarity to known antibiotics reported from members of the genus, Nonomuraea. As the trends to discover novel metabolites from Nonomuraea are vibrant, further studies are needed to understand the structural and biotechnological significance of antibiotic compound produced by Nonomuraea sp. JAJ18.
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Affiliation(s)
- Polpass Arul Jose
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai 625 021, India
| | | | - Pandiyan Rajeswari
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai 625 021, India
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Jose PA, Jebakumar SRD. Non-streptomycete actinomycetes nourish the current microbial antibiotic drug discovery. Front Microbiol 2013; 4:240. [PMID: 23970883 PMCID: PMC3747354 DOI: 10.3389/fmicb.2013.00240] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 07/31/2013] [Indexed: 11/17/2022] Open
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