201
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Niu X, Chen L, Yue Q, Wang B, Zhang J, Zhu C, Zhang K, Bills GF, An Z. Characterization of Thermolide Biosynthetic Genes and a New Thermolide from Sister Thermophilic Fungi. Org Lett 2014; 16:3744-7. [DOI: 10.1021/ol501595z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xuemei Niu
- Texas
Therapeutics Institute, the Brown Foundation Institute of Molecular
Medicine, the University of Texas Health Science Center at Houston, Houston, Texas 77054, United States
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Li Chen
- Texas
Therapeutics Institute, the Brown Foundation Institute of Molecular
Medicine, the University of Texas Health Science Center at Houston, Houston, Texas 77054, United States
| | - Qun Yue
- Texas
Therapeutics Institute, the Brown Foundation Institute of Molecular
Medicine, the University of Texas Health Science Center at Houston, Houston, Texas 77054, United States
| | - Baile Wang
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | | | - Chunyan Zhu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Keqin Zhang
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Gerald F. Bills
- Texas
Therapeutics Institute, the Brown Foundation Institute of Molecular
Medicine, the University of Texas Health Science Center at Houston, Houston, Texas 77054, United States
| | - Zhiqiang An
- Texas
Therapeutics Institute, the Brown Foundation Institute of Molecular
Medicine, the University of Texas Health Science Center at Houston, Houston, Texas 77054, United States
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202
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203
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Biosynthesis of crocacin involves an unusual hydrolytic release domain showing similarity to condensation domains. ACTA ACUST UNITED AC 2014; 21:855-65. [PMID: 24981773 DOI: 10.1016/j.chembiol.2014.05.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/12/2014] [Accepted: 05/15/2014] [Indexed: 11/20/2022]
Abstract
The crocacins are potent antifungal and cytotoxic natural compounds from myxobacteria of the genus Chondromyces. Although total synthesis approaches have been reported, the molecular and biochemical basis guiding the formation of the linear crocacin scaffold has remained unknown. Along with the identification and functional analysis of the crocacin biosynthetic gene cluster from Chondromyces crocatus Cm c5, we here present the identification and biochemical characterization of an unusual chain termination domain homologous to condensation domains responsible for hydrolytic release of the product from the assembly line. In particular, gene inactivation studies and in vitro experiments using the heterologously produced domain CroK-C2 confirm this surprising role giving rise to the linear carboxylic acid. Additionally, we determined the kinetic parameters of CroK-C2 by monitoring hydrolytic cleavage of the substrate mimic N-acetylcysteaminyl-crocacin B using an innovative high-performance liquid chromatography mass spectrometry-based assay.
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204
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Sun D, Sun W, Yu Y, Li Z, Deng Z, Lin S. A new glutarimide derivative from marine sponge-derived Streptomyces anulatus S71. Nat Prod Res 2014; 28:1602-6. [DOI: 10.1080/14786419.2014.928877] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Dandan Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
| | - Wei Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
| | - Yinxian Yu
- Department of Orthopedic Surgery, Shanghai Frist People's Hospital, School of Medicine, Shanghai Jiao Tong University, 100 Haining Road, Shanghai 200080, P.R. China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P.R. China
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205
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Li Y, Chen H, Ding Y, Xie Y, Wang H, Cerny RL, Shen Y, Du L. Iterative Assembly of Two Separate Polyketide Chains by the Same Single-Module Bacterial Polyketide Synthase in the Biosynthesis of HSAF. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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206
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Zhang J, Qian Z, Wu X, Ding Y, Li J, Lu C, Shen Y. Juanlimycins A and B, Ansamycin Macrodilactams from Streptomyces sp. Org Lett 2014; 16:2752-5. [PMID: 24797062 DOI: 10.1021/ol501072t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juanli Zhang
- Key
Laboratory of Chemical Biology (Ministry of Education), School of
Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Zhengyi Qian
- State
Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, No. 27 South Shanda Road, Jinan, Shandong 250100, PR China
| | - Xingkang Wu
- Key
Laboratory of Chemical Biology (Ministry of Education), School of
Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Yanjiao Ding
- Key
Laboratory of Chemical Biology (Ministry of Education), School of
Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Jianfang Li
- Key
Laboratory of Chemical Biology (Ministry of Education), School of
Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong 250012, PR China
- School
of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, PR China
| | - Chunhua Lu
- Key
Laboratory of Chemical Biology (Ministry of Education), School of
Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Yuemao Shen
- Key
Laboratory of Chemical Biology (Ministry of Education), School of
Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong 250012, PR China
- State
Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, No. 27 South Shanda Road, Jinan, Shandong 250100, PR China
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207
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Maspoli A, Wenner N, Mislin GLA, Reimmann C. Functional analysis of pyochelin-/enantiopyochelin-related genes from a pathogenicity island of Pseudomonas aeruginosa strain PA14. Biometals 2014; 27:559-73. [PMID: 24682869 DOI: 10.1007/s10534-014-9729-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 03/17/2014] [Indexed: 05/28/2023]
Abstract
Genomic islands are foreign DNA blocks inserted in so-called regions of genomic plasticity (RGP). Depending on their gene content, they are classified as pathogenicity, symbiosis, metabolic, fitness or resistance islands, although a detailed functional analysis is often lacking. Here we focused on a 34-kb pathogenicity island of Pseudomonas aeruginosa PA14 (PA14GI-6), which is inserted at RGP5 and carries genes related to those for pyochelin/enantiopyochelin biosynthesis. These enantiomeric siderophores of P. aeruginosa and certain strains of Pseudomonas protegens are assembled by a thiotemplate mechanism from salicylate and two molecules of cysteine. The biochemical function of several proteins encoded by PA14GI-6 was investigated by a series of complementation analyses using mutants affected in potential homologs. We found that PA14_54940 codes for a bifunctional salicylate synthase/salicyl-AMP ligase (for generation and activation of salicylate), that PA14_54930 specifies a dihydroaeruginoic acid (Dha) synthetase (for coupling salicylate with a cysteine-derived thiazoline ring), that PA14_54910 produces a type II thioesterase (for quality control), and that PA14_54880 encodes a serine O-acetyltransferase (for increased cysteine availability). The structure of the PA14GI-6-specified metabolite was determined by mass spectrometry, thin-layer chromatography, and HPLC as (R)-Dha, an iron chelator with antibacterial, antifungal and antitumor activity. The conservation of this genomic island in many clinical and environmental P. aeruginosa isolates of different geographical origin suggests that the ability for Dha production may confer a selective advantage to its host.
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Affiliation(s)
- Alessandro Maspoli
- Département de Microbiologie Fondamentale, Université de Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, 1015, Lausanne, Switzerland
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208
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He HY, Tang MC, Zhang F, Tang GL. Cis-Double Bond Formation by Thioesterase and Transfer by Ketosynthase in FR901464 Biosynthesis. J Am Chem Soc 2014; 136:4488-91. [DOI: 10.1021/ja500942y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hai-Yan He
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Man-Cheng Tang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Feng Zhang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong-Li Tang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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209
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Djukic M, Brzuszkiewicz E, Fünfhaus A, Voss J, Gollnow K, Poppinga L, Liesegang H, Garcia-Gonzalez E, Genersch E, Daniel R. How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae. PLoS One 2014; 9:e90914. [PMID: 24599066 PMCID: PMC3944939 DOI: 10.1371/journal.pone.0090914] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 02/05/2014] [Indexed: 12/20/2022] Open
Abstract
Paenibacillus larvae, a Gram positive bacterial pathogen, causes American Foulbrood (AFB), which is the most serious infectious disease of honey bees. In order to investigate the genomic potential of P. larvae, two strains belonging to two different genotypes were sequenced and used for comparative genome analysis. The complete genome sequence of P. larvae strain DSM 25430 (genotype ERIC II) consisted of 4,056,006 bp and harbored 3,928 predicted protein-encoding genes. The draft genome sequence of P. larvae strain DSM 25719 (genotype ERIC I) comprised 4,579,589 bp and contained 4,868 protein-encoding genes. Both strains harbored a 9.7 kb plasmid and encoded a large number of virulence-associated proteins such as toxins and collagenases. In addition, genes encoding large multimodular enzymes producing nonribosomally peptides or polyketides were identified. In the genome of strain DSM 25719 seven toxin associated loci were identified and analyzed. Five of them encoded putatively functional toxins. The genome of strain DSM 25430 harbored several toxin loci that showed similarity to corresponding loci in the genome of strain DSM 25719, but were non-functional due to point mutations or disruption by transposases. Although both strains cause AFB, significant differences between the genomes were observed including genome size, number and composition of transposases, insertion elements, predicted phage regions, and strain-specific island-like regions. Transposases, integrases and recombinases are important drivers for genome plasticity. A total of 390 and 273 mobile elements were found in strain DSM 25430 and strain DSM 25719, respectively. Comparative genomics of both strains revealed acquisition of virulence factors by horizontal gene transfer and provided insights into evolution and pathogenicity.
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Affiliation(s)
- Marvin Djukic
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Elzbieta Brzuszkiewicz
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Anne Fünfhaus
- Department for Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Jörn Voss
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Kathleen Gollnow
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Lena Poppinga
- Department for Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Eva Garcia-Gonzalez
- Department for Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Elke Genersch
- Department for Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
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210
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Wang M, Beissner M, Zhao H. Aryl-aldehyde formation in fungal polyketides: discovery and characterization of a distinct biosynthetic mechanism. CHEMISTRY & BIOLOGY 2014; 21:257-63. [PMID: 24412543 PMCID: PMC3943900 DOI: 10.1016/j.chembiol.2013.12.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 12/02/2013] [Accepted: 12/07/2013] [Indexed: 11/22/2022]
Abstract
Aryl-aldehydes are a common feature in fungal polyketides, which are considered to be exclusively generated by the R domain of nonreducing polyketide synthases (NR-PKSs). However, by cloning and heterologous expression of both cryptic NR-PKS and nonribosomal peptide synthase (NRPS)-like genes from Aspergillus terreus in Saccharomyces cerevisiae, we identified a distinct mechanism for aryl-aldehyde formation in which a NRPS-like protein activates and reduces an aryl-acid produced by the accompanying NR-PKS to an aryl-aldehyde. Bioinformatics study indicates that such a mechanism may be widely used throughout the fungi kingdom.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mirko Beissner
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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211
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Gaudelli NM, Townsend CA. Epimerization and substrate gating by a TE domain in β-lactam antibiotic biosynthesis. Nat Chem Biol 2014; 10:251-8. [PMID: 24531841 PMCID: PMC3961552 DOI: 10.1038/nchembio.1456] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/30/2013] [Indexed: 12/01/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are versatile engines of bioactive natural product biosynthesis that function according to the multiple carrier thiotemplate mechanism. C-terminal thioesterase (TE) domains of these giant modular proteins typically catalyze product release by hydrolysis or macrocylization. We now report an unprecedented, dual-function TE involved in nocardicin A biosynthesis, the paradigm monocyclic β-lactam antibiotic. Contrary to expectation, a stereodefined series of potential peptide substrates for the nocardicin TE domain failed to undergo hydrolysis. The stringent discrimination against peptide intermediates was dramatically overcome by prior monocyclic β-lactam formation at an L-seryl site. Kinetic data are interpreted such that the TE domain acts as a gatekeeper to hold the assembling peptide on an upstream domain until β-lactam formation takes place and then rapidly catalyzes epimerization, not previously observed as a TE catalytic function, and thioesterase cleavage to discharge a fully fledged pentapeptide β-lactam harboring nocardicin G, the universal precursor of the nocardicins.
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Affiliation(s)
- Nicole M Gaudelli
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
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212
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Collemare J, Griffiths S, Iida Y, Karimi Jashni M, Battaglia E, Cox RJ, de Wit PJGM. Secondary metabolism and biotrophic lifestyle in the tomato pathogen Cladosporium fulvum. PLoS One 2014; 9:e85877. [PMID: 24465762 PMCID: PMC3895014 DOI: 10.1371/journal.pone.0085877] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/03/2013] [Indexed: 01/07/2023] Open
Abstract
Cladosporium fulvum is a biotrophic fungal pathogen that causes leaf mould of tomato. Analysis of its genome suggested a high potential for production of secondary metabolites (SM), which might be harmful to plants and animals. Here, we have analysed in detail the predicted SM gene clusters of C. fulvum employing phylogenetic and comparative genomic approaches. Expression of the SM core genes was measured by RT-qrtPCR and produced SMs were determined by LC-MS and NMR analyses. The genome of C. fulvum contains six gene clusters that are conserved in other fungal species, which have undergone rearrangements and gene losses associated with the presence of transposable elements. Although being a biotroph, C. fulvum has the potential to produce elsinochrome and cercosporin toxins. However, the corresponding core genes are not expressed during infection of tomato. Only two core genes, PKS6 and NPS9, show high expression in planta, but both are significantly down regulated during colonization of the mesophyll tissue. In vitro SM profiling detected only one major compound that was identified as cladofulvin. PKS6 is likely involved in the production of this pigment because it is the only core gene significantly expressed under these conditions. Cladofulvin does not cause necrosis on Solanaceae plants and does not show any antimicrobial activity. In contrast to other biotrophic fungi that have a reduced SM production capacity, our studies on C. fulvum suggest that down-regulation of SM biosynthetic pathways might represent another mechanism associated with a biotrophic lifestyle.
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Affiliation(s)
- Jérôme Collemare
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Centre for Biosystems Genomics, Wageningen, The Netherlands
- * E-mail:
| | - Scott Griffiths
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Yuichiro Iida
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- National Institute of Vegetable and Tea Science, Tsu, Japan
| | - Mansoor Karimi Jashni
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran
| | - Evy Battaglia
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Russell J. Cox
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Pierre J. G. M. de Wit
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Centre for Biosystems Genomics, Wageningen, The Netherlands
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213
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Della Sala G, Hochmuth T, Costantino V, Teta R, Gerwick W, Gerwick L, Piel J, Mangoni A. Polyketide genes in the marine sponge Plakortis simplex: a new group of mono-modular type I polyketide synthases from sponge symbionts. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:809-818. [PMID: 24249289 PMCID: PMC3908369 DOI: 10.1111/1758-2229.12081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 06/22/2013] [Indexed: 05/31/2023]
Abstract
Sponge symbionts are a largely unexplored source of new and unusual metabolic pathways. Insights into the distribution and function of metabolic genes of sponge symbionts are crucial to dissect and exploit their biotechnological potential. Screening of the metagenome of the marine sponge Plakortis simplex led to the discovery of the swf family, a new group of mono-modular type I polyketide synthase/fatty acid synthase (PKS/FAS) specifically associated with sponge symbionts. Two different examples of the swf cluster were present in the metagenome of P. simplex. A third example of the cluster is present in the previously sequenced genome of a poribacterium from the sponge Aplysina aerophoba but was formerly considered orthologous to the wcb/rkp cluster. The swf cluster was also found in six additional species of sponges. Therefore, the swf cluster represents the second group of mono-modular PKS, after the supA family, to be widespread in marine sponges. The putative swf operon consists of swfA (type I PKS/FAS), swfB (reductase and sulphotransferase domains) and swfC (radical S-adenosylmethionine, or radical SAM). Activation of the acyl carrier protein (ACP) domain of the SwfA protein to its holo-form by co-expression with Svp is the first functional proof of swf type genes in marine sponges. However, the precise biosynthetic role of the swf clusters remains unknown.
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Affiliation(s)
- Gerardo Della Sala
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - Thomas Hochmuth
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - Valeria Costantino
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - Roberta Teta
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - William Gerwick
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego9500 Gilman Drive, MC 0212, La Jolla, CA, 92093-0212, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego9500 Gilman Drive, MC 0212, La Jolla, CA, 92093-0212, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenoessische Technische Hochschule (ETH) ZurichWolfgang-Pauli-Str. 10, 8093, Zurich, Switzerland
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
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214
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Fahad AA, Abood A, Fisch KM, Osipow A, Davison J, Avramović M, Butts CP, Piel J, Simpson TJ, Cox RJ. Oxidative dearomatisation: the key step of sorbicillinoid biosynthesis†Electronic supplementary information (ESI) available: Containing all experimental details. See DOI: 10.1039/c3sc52911hClick here for additional data file. Chem Sci 2013; 5:523-527. [PMID: 25580210 PMCID: PMC4285102 DOI: 10.1039/c3sc52911h] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 11/15/2013] [Indexed: 11/21/2022] Open
Abstract
A new biosynthetic pathway to the sorbicillinoid natural products is proposed based on the observation of oxidative dearomatisation of dihydrosorbicillin 10b.
An FAD-dependent monooxygenase encoding gene (SorbC) was cloned from Penicillium chrysogenum E01-10/3 and expressed as a soluble protein in Escherichia coli. The enzyme efficiently performed the oxidative dearomatisation of sorbicillin and dihydrosorbicillin to give sorbicillinol and dihydrosorbicillinol respectively. Bioinformatic examination of the gene cluster surrounding SorbC indicated the presence of two polyketide synthase (PKS) encoding genes designated sorbA and sorbB. The gene sorbA-encodes a highly reducing iterative PKS while SorbB encodes a non-reducing iterative PKS which features a reductive release domain usually involved in the production of polyketide aldehydes. Using these observations and previously reported results from isotopic feeding experiments a new and simpler biosynthetic route to the sorbicillin class of secondary metabolites is proposed which is consistent with all reported experimental results.
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Affiliation(s)
- Ahmed Al Fahad
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; ; Tel: +44 (0) 117 928 9184
| | - Amira Abood
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; ; Tel: +44 (0) 117 928 9184 ; Chemistry of Natural and Microbial Products , National Research Centre , Dokki , Egypt
| | - Katja M Fisch
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; ; Tel: +44 (0) 117 928 9184
| | - Anna Osipow
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; ; Tel: +44 (0) 117 928 9184
| | - Jack Davison
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; ; Tel: +44 (0) 117 928 9184
| | - Marija Avramović
- Institute of Microbiology , Eidgenössische Technische Hochschule (ETH) Zürich , Wolfgang-Pauli-Str. 10 , 8093 Zürich , Switzerland
| | - Craig P Butts
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; ; Tel: +44 (0) 117 928 9184
| | - Jörn Piel
- Institute of Microbiology , Eidgenössische Technische Hochschule (ETH) Zürich , Wolfgang-Pauli-Str. 10 , 8093 Zürich , Switzerland ; Kekulé Institute of Organic Chemistry and Biochemistry , University of Bonn , Gerhard-Domagk-Str. 1 , 53121 Bonn , Germany
| | - Thomas J Simpson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; ; Tel: +44 (0) 117 928 9184
| | - Russell J Cox
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ; ; Tel: +44 (0) 117 928 9184 ; Institut für Organische Chemie , Leibniz Universität Hannover , Schneiderberg 1B , 30167 Hannover , Germany .
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215
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Mantovani SM, Moore BS. Flavin-linked oxidase catalyzes pyrrolizine formation of dichloropyrrole-containing polyketide extender unit in chlorizidine A. J Am Chem Soc 2013; 135:18032-5. [PMID: 24246014 DOI: 10.1021/ja409520v] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The marine alkaloid chlorizidine A contains chlorinated pyrroloisoindolone and pyrrolizine rings that are rare chemical features in bacterial natural products. Herein, we report the biosynthetic logic of their construction in Streptomyces sp. CNH-287 based on the identification of the chlorizidine A biosynthetic gene cluster. Using whole pathway heterologous expression and genetic manipulations, we show that chlorizidine A is assembled by a polyketide synthase that uniquely incorporates a fatty acid synthase-derived dichloropyrrolyl extender unit into the pyrroloisoindolone enzymatic product. We further provide the first biochemical characterization of a flavoenzyme associated with the oxidative formation of chlorizidine A's distinctive pyrrolizine ring. This work illuminates new enzymatic assembly line processes leading to rare nitrogen-containing rings in nature.
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Affiliation(s)
- Simone M Mantovani
- Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego, California 92093, United States
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216
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Harnessing the potential of halogenated natural product biosynthesis by mangrove-derived actinomycetes. Mar Drugs 2013; 11:3875-90. [PMID: 24129229 PMCID: PMC3826140 DOI: 10.3390/md11103875] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 12/30/2022] Open
Abstract
Mangrove-derived actinomycetes are promising sources of bioactive natural products. In this study, using homologous screening of the biosynthetic genes and anti-microorganism/tumor assaying, 163 strains of actinomycetes isolated from mangrove sediments were investigated for their potential to produce halogenated metabolites. The FADH2-dependent halogenase genes, identified in PCR-screening, were clustered in distinct clades in the phylogenetic analysis. The coexistence of either polyketide synthase (PKS) or nonribosomal peptide synthetase (NRPS) as the backbone synthetases in the strains harboring the halogenase indicated that these strains had the potential to produce structurally diversified antibiotics. As a validation, a new enduracidin producer, Streptomyces atrovirens MGR140, was identified and confirmed by gene disruption and HPLC analysis. Moreover, a putative ansamycin biosynthesis gene cluster was detected in Streptomyces albogriseolus MGR072. Our results highlight that combined genome mining is an efficient technique to tap promising sources of halogenated natural products synthesized by mangrove-derived actinomycetes.
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217
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Sequence characterization and computational analysis of the non-ribosomal peptide synthetases controlling biosynthesis of lipopeptides, fengycins and bacillomycin D, from Bacillus amyloliquefaciens Q-426. Biotechnol Lett 2013; 35:2155-63. [PMID: 24068498 DOI: 10.1007/s10529-013-1320-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Abstract
Lipopeptides secreted by bacteria attract interest because of their uses in biomedicine, biotechnology and food technology; however, harnessing their megasynthases (non-ribosomal peptide synthetases, NRPSs) has met with some difficulties in heterologous expression and crystallization. Here, we used similarity and phylogenetic analysis of NRPS sequences, including the fengycin and iturin family synthetases from Bacillus spp., and have developed a novel approach for delineating the length and boundaries of NRPS domains from Bacillus amyloliquefaciens strain Q-426. The sequences were further characterized (including specific residues and conserved motifs) that gave insight into the basis of the substrate specificity. Data from the prediction of the NRPS domains, obtained by the self-optimized prediction method with Alignment program, showed they are all structurally unstable, making it difficult to determine their crystal structures.
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218
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Belecki K, Townsend CA. Biochemical determination of enzyme-bound metabolites: preferential accumulation of a programmed octaketide on the enediyne polyketide synthase CalE8. J Am Chem Soc 2013; 135:14339-48. [PMID: 24041368 DOI: 10.1021/ja406697t] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite considerable interest in the enediyne family of antitumor antibiotics, assembly of their polyketide core structures in nature remains poorly understood. Discriminating methods to access enzyme-bound intermediates are critical for elucidating unresolved polyketide and nonribosomal peptide biosynthetic pathways. Here, we describe the development of broadly applicable techniques for the mild chemical release and analysis of intermediates bound to carrier proteins (CPs), providing access to these species even in sensitive systems. These techniques were applied to CalE8, the polyketide synthase (PKS) involved in calicheamicin biosynthesis, facilitating the unambiguous identification of enzyme-bound polyketides on an enediyne PKS. Moreover, these methods enabled the preparation of fully unloaded CalE8, providing a "clean slate" for reconstituted activity and allowing us to demonstrate the preferential accumulation of a PKS-bound octaketide with evidence of programmed processing control by CalE8. This intermediate, which has the expected chain length for enediyne core construction, could previously only be indirectly inferred. These studies prove that this polyketide is an authentic product of CalE8 and may be a key precursor to the enediyne core of calicheamicin, as it is the only programmed, enzyme-bound species observed for any enediyne system to date. Our experimental advances into a generally inaccessible system illustrate the utility of these techniques for investigating CP-based biosynthetic pathways.
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Affiliation(s)
- Katherine Belecki
- Department of Chemistry, The Johns Hopkins University , Remsen 252, 3400 North Charles St., Baltimore, Maryland 21218, United States
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219
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Du YL, Dalisay DS, Andersen RJ, Ryan KS. N-carbamoylation of 2,4-diaminobutyrate reroutes the outcome in padanamide biosynthesis. ACTA ACUST UNITED AC 2013; 20:1002-11. [PMID: 23911586 DOI: 10.1016/j.chembiol.2013.06.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/05/2013] [Accepted: 06/25/2013] [Indexed: 01/07/2023]
Abstract
Padanamides are linear tetrapeptides notable for the absence of proteinogenic amino acids in their structures. In particular, two unusual heterocycles, (S)-3-amino-2-oxopyrrolidine-1-carboxamide (S-Aopc) and (S)-3-aminopiperidine-2,6-dione (S-Apd), are found at the C-termini of padanamides A and B, respectively. Here we identify the padanamide biosynthetic gene cluster and carry out systematic gene inactivation studies. Our results show that padanamides are synthesized by highly dissociated hybrid nonribosomal peptide synthetase/polyketide synthase machinery. We further demonstrate that carbamoyltransferase gene padQ is critical to the formation of padanamide A but dispensable for biosynthesis of padanamide B. Biochemical investigations show that PadQ carbamoylates the rare biosynthetic precursor l-2,4-diaminobutyrate, generating l-2-amino-4-ureidobutyrate, the presumed precursor to the C-terminal residue of padanamide A. By contrast, the C-terminal residue of padanamide B may derive from glutamine. An unusual thioesterase-catalyzed cyclization is proposed to generate the S-Aopc/S-Apd heterocycles.
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Affiliation(s)
- Yi-Ling Du
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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220
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Xu Y, Zhou T, Zhang S, Xuan LJ, Zhan J, Molnár I. Thioesterase domains of fungal nonreducing polyketide synthases act as decision gates during combinatorial biosynthesis. J Am Chem Soc 2013; 135:10783-91. [PMID: 23822773 PMCID: PMC3780601 DOI: 10.1021/ja4041362] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A crucial step during the programmed biosynthesis of fungal polyketide natural products is the release of the final polyketide intermediate from the iterative polyketide synthases (iPKSs), most frequently by a thioesterase (TE) domain. Realization of combinatorial biosynthesis with iPKSs requires TE domains that can accept altered polyketide intermediates generated by hybrid synthase enzymes and successfully release "unnatural products" with the desired structure. Achieving precise control over product release is of paramount importance with O-C bond-forming TE domains capable of macrocyclization, hydrolysis, transesterification, and pyrone formation that channel reactive, pluripotent polyketide intermediates to defined structural classes of bioactive secondary metabolites. By exploiting chimeric iPKS enzymes to offer substrates with controlled structural variety to two orthologous O-C bond-forming TE domains in situ, we show that these enzymes act as nonequivalent decision gates, determining context-dependent release mechanisms and overall product flux. Inappropriate choice of a TE could eradicate product formation in an otherwise highly productive chassis. Conversely, a judicious choice of a TE may allow the production of a desired hybrid metabolite. Finally, a serendipitous choice of a TE may reveal the unexpected productivity of some chassis. The ultimate decision gating role of TE domains influences the observable outcome of combinatorial domain swaps, emphasizing that the deduced programming rules are context dependent. These factors may complicate engineering the biosynthesis of a desired "unnatural product" but may also open additional avenues to create biosynthetic novelty based on fungal nonreduced polyketides.
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Affiliation(s)
- Yuquan Xu
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Tong Zhou
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322, USA
| | - Shuwei Zhang
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322, USA
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Li-Jiang Xuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Jixun Zhan
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322, USA
| | - István Molnár
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
- Bio5 Institute, The University of Arizona, 1657 E. Helen St., Tucson, AZ 85721, USA
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221
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Chen Y, McClure RA, Zheng Y, Thomson RJ, Kelleher NL. Proteomics guided discovery of flavopeptins: anti-proliferative aldehydes synthesized by a reductase domain-containing non-ribosomal peptide synthetase. J Am Chem Soc 2013; 135:10449-56. [PMID: 23763305 DOI: 10.1021/ja4031193] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Due to the importance of proteases in regulating cellular processes, the development of protease inhibitors has garnered great attention. Peptide-based aldehydes are a class of compounds that exhibit inhibitory activities against various proteases and proteasomes in the context of anti-proliferative treatments for cancer and other diseases. More than a dozen peptide-based natural products containing aldehydes have been discovered such as chymostatin, leupeptin, and fellutamide; however, the biosynthetic origin of the aldehyde functionality has yet to be elucidated. Herein we describe the discovery of a new group of lipopeptide aldehydes, the flavopeptins, and the corresponding biosynthetic pathway arising from an orphan gene cluster in Streptomyces sp. NRRL-F6652, a close relative of Streptomyces flavogriseus ATCC 33331. This research was initiated using a proteomics approach that screens for expressed enzymes involved in secondary metabolism in microorganisms. Flavopeptins are synthesized through a non-ribosomal peptide synthetase containing a terminal NAD(P)H-dependent reductase domain likely for the reductive release of the peptide with a C-terminal aldehyde. Solid-phase peptide synthesis of several flavopeptin species and derivatives enabled structural verification and subsequent screening of biological activity. Flavopeptins exhibit sub-micromolar inhibition activities against cysteine proteases such as papain and calpain as well as the human 20S proteasome. They also show anti-proliferative activities against multiple myeloma and lymphoma cell lines.
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Affiliation(s)
- Yunqiu Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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222
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Yu D, Xu F, Zi J, Wang S, Gage D, Zeng J, Zhan J. Engineered production of fungal anticancer cyclooligomer depsipeptides in Saccharomyces cerevisiae. Metab Eng 2013; 18:60-8. [DOI: 10.1016/j.ymben.2013.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 01/21/2013] [Accepted: 04/01/2013] [Indexed: 11/24/2022]
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223
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Shionozaki N, Iwamura N, Tanaka R, Makino K, Uchiro H. Total synthesis of diaporthichalasin by using the intramolecular Diels-Alder reaction of an α,β-unsaturated γ-hydroxylactam in aqueous media. Chem Asian J 2013; 8:1243-52. [PMID: 23554293 DOI: 10.1002/asia.201201230] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Indexed: 11/07/2022]
Abstract
The first total synthesis of diaporthichalasin has been successfully achieved and complete structure elucidation, including the absolute configuration, was also accomplished. The intramolecular Diels-Alder (IMDA) reaction between the diene side chain on the decalin skeleton and α,β-unsaturated γ-hydroxy-γ-lactam in aqueous media was effectively employed as the key step. From this synthetic study, we found that α,β-unsaturated γ-hydroxy-γ-lactam is an essential precursor for the construction of the diaporthichalasin-type pentacyclic skeleton. This important finding strongly suggests that this route is involved in the biosynthetic pathway for diaporthichalasin.
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Affiliation(s)
- Nobuhiro Shionozaki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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224
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Cyclization of fungal nonribosomal peptides by a terminal condensation-like domain. Nat Chem Biol 2013; 8:823-30. [PMID: 22902615 PMCID: PMC3505271 DOI: 10.1038/nchembio.1047] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 07/03/2012] [Indexed: 12/13/2022]
Abstract
Cyclization of linear peptidyl precursors produced by nonribosomal peptide synthetases (NRPSs) is an important step in the biosynthesis of bioactive cyclic peptides. Whereas bacterial NRPSs use thioesterase (TE) domains to perform the cyclization, fungal NRPSs have apparently evolved to use a different enzymatic route. In verified fungal NRPSs that produce macrocyclic peptides, each megasynthetase terminates with a condensation-like (CT) domain that may perform the macrocyclization reaction. To probe the role of such a CT domain, we reconstituted the activities of the Penicillium aethiopicum trimodular NPRS TqaA in Saccharomyces cerevisiae and in vitro. Together with a reconstituted bimodular NRPS AnaPS, we dissected the cyclization steps of TqaA in transforming the linear anthranilate-D-tryptophan-L-alanyl tripeptide into fumiquinazoline F. Extensive biochemical and mutational studies confirmed the essential role of the CT domain in catalyzing cyclization in a thiolation domain-dependent fashion. Our work provided evidence of a likely universal macrocyclization strategy employed by fungal NRPSs.
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225
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Tang MC, He HY, Zhang F, Tang GL. Baeyer–Villiger Oxidation of Acyl Carrier Protein-Tethered Thioester to Acyl Carrier Protein-Linked Thiocarbonate Catalyzed by a Monooxygenase Domain in FR901464 Biosynthesis. ACS Catal 2013. [DOI: 10.1021/cs300819e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Man-Cheng Tang
- State Key
Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032,
China
| | - Hai-Yan He
- State Key
Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032,
China
| | - Feng Zhang
- State Key
Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032,
China
| | - Gong-Li Tang
- State Key
Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032,
China
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226
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Wilson DJ, Shi C, Teitelbaum AM, Gulick AM, Aldrich CC. Characterization of AusA: a dimodular nonribosomal peptide synthetase responsible for the production of aureusimine pyrazinones. Biochemistry 2013; 52:926-37. [PMID: 23302043 PMCID: PMC3577359 DOI: 10.1021/bi301330q] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aureusimines have been identified as potential virulence factors in Staphylococcus aureus. These pyrazinone secondary metabolites are produced by a nonribosomal peptide synthetase (NRPS) annotated as AusA. We report the overproduction of AusA as a 277 kDa soluble protein with A(1)-T(1)-C-A(2)-T(2)-R bimodular architecture. The substrate specificity of each adenylation (A) domain was initially probed using an ATP-pyrophosphate exchange assay with A-domain selective bisubstrate inhibitors to chemically knock out each companion A-domain. The activity of AusA was then reconstituted in vitro and shown to produce all naturally occurring aureusimines and non-natural pyrazinone products with k(cat) values ranging from 0.4 to 1.3 min(-1). Steady-state kinetic parameters were determined for all substrates and cofactors, providing the first comprehensive steady-state characterization of a NRPS employing a product formation assay. The K(M) values for the amino acids were up to 60-fold lower with the product formation assay than with the ATP-pyrophosphate exchange assay, most commonly used to assess A-domain substrate specificity. The C-terminal reductase (R) domain catalyzes reductive release of the dipeptidyl intermediate, leading to formation of an amino aldehyde that cyclizes to a dihydropyrazinone. We show oxidation to the final pyrazinone heterocycle is spontaneous. The activity and specificity of the R-domain was independently investigated using a NADPH consumption assay. AusA is a minimal autonomous two-module NRPS that represents an excellent model system for further kinetic and structural characterization.
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Affiliation(s)
- Daniel J. Wilson
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455
| | - Ce Shi
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455
| | - Aaron M. Teitelbaum
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, MN 55455
| | - Andrew M. Gulick
- Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY, 14203 USA
| | - Courtney C. Aldrich
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455
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227
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Kohlhaas C, Jenner M, Kampa A, Briggs GS, Afonso JP, Piel J, Oldham NJ. Amino acid-accepting ketosynthase domain from a trans-AT polyketide synthase exhibits high selectivity for predicted intermediate. Chem Sci 2013. [DOI: 10.1039/c3sc50540e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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228
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229
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Xu W, Qiao K, Tang Y. Structural analysis of protein-protein interactions in type I polyketide synthases. Crit Rev Biochem Mol Biol 2012; 48:98-122. [PMID: 23249187 DOI: 10.3109/10409238.2012.745476] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Polyketide synthases (PKSs) are responsible for synthesizing a myriad of natural products with agricultural, medicinal relevance. The PKSs consist of multiple functional domains of which each can catalyze a specified chemical reaction leading to the synthesis of polyketides. Biochemical studies showed that protein-substrate and protein-protein interactions play crucial roles in these complex regio-/stereo-selective biochemical processes. Recent developments on X-ray crystallography and protein NMR techniques have allowed us to understand the biosynthetic mechanism of these enzymes from their structures. These structural studies have facilitated the elucidation of the sequence-function relationship of PKSs and will ultimately contribute to the prediction of product structure. This review will focus on the current knowledge of type I PKS structures and the protein-protein interactions in this system.
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Affiliation(s)
- Wei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
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230
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Lange A, Sun H, Pilger J, Reinscheid UM, Gross H. Predicting the structure of cyclic lipopeptides by bioinformatics: structure revision of arthrofactin. Chembiochem 2012; 13:2671-5. [PMID: 23169772 DOI: 10.1002/cbic.201200532] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Indexed: 11/09/2022]
Abstract
Arthrofactin, a bioactive cyclic lipopeptide from Pseudomonas sp. MIS38, was reinvestigated for its structural and stereochemical features due to discrepancies between the genetics-based sequence prediction and the currently suggested structure. The structure of arthrofactin and its derivatives was reassigned on the basis of chiral HPLC analysis and extensive NMR and MS experiments. Furthermore, derivatives of arthrofactin were discovered.
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Affiliation(s)
- Anna Lange
- Institute for Pharmaceutical Biology, University of Bonn, Germany
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231
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Abstract
The iterative type I polyketide synthases (IPKSs) are central to the biosynthesis of an enormously diverse array of natural products in fungi. These natural products, known as polyketides, exhibit a wide range of biological activities and include clinically important drugs as well as undesirable toxins. The PKSs synthesize these structurally diverse polyketides via a series of decarboxylative condensations of malonyl-CoA extender units and β-keto modifications in a highly programmed manner. Significant progress has been made over the past few years in understanding the biosynthetic mechanism and programming of fungal PKSs. The continuously expanding fungal genome sequence data have sparked genome-directed discoveries of new fungal PKSs and associated products. The increasing number of fungal PKSs that have been linked to their products along with in-depth biochemical and structural characterizations of these large enzymes have remarkably improved our knowledge on the molecular basis for polyketide structural diversity in fungi. This Perspective highlights the recent advances and examines how the newly expanded paradigm has contributed to our ability to link fungal PKS genes to chemical structures and vice versa. The knowledge will help us navigate through the logarithmically expanding seas of genomic information for polyketide compound discovery and provided opportunities to reprogram these megasynthases to generate new chemical entities.
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Affiliation(s)
- Yit-Heng Chooi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
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232
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Belecki K, Townsend CA. Environmental Control of the Calicheamicin Polyketide Synthase Leads to Detection of a Programmed Octaketide and a Proposal for Enediyne Biosynthesis. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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233
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Newman AG, Vagstad AL, Belecki K, Scheerer JR, Townsend CA. Analysis of the cercosporin polyketide synthase CTB1 reveals a new fungal thioesterase function. Chem Commun (Camb) 2012; 48:11772-4. [PMID: 23108075 DOI: 10.1039/c2cc36010a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The polyketide synthase CTB1 is demonstrated to catalyze pyrone formation thereby expanding the known biosynthetic repertoire of thioesterase domains in iterative, non-reducing polyketide synthases.
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Affiliation(s)
- Adam G Newman
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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234
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Detection and purification of non-ribosomal peptide synthetase products in Neosartorya fischeri. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 944:111-9. [PMID: 23065611 DOI: 10.1007/978-1-62703-122-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are important enzymes of production machinery for natural products including clinically used antibiotics, antifungal, and anticancer agents. NRPS products are usually further modified by tailoring enzymes, resulting in the formation of diverse structures. We demonstrate here the production and isolation of metabolites produced by two bi-modular NRPSs, i.e., acetylaszonalenin and fumitremorgin-type alkaloids in Neosartorya fischeri NRRL181.
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235
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Wyatt MA, Mok MCY, Junop M, Magarvey NA. Heterologous expression and structural characterisation of a pyrazinone natural product assembly line. Chembiochem 2012; 13:2408-15. [PMID: 23070851 DOI: 10.1002/cbic.201200340] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Indexed: 11/07/2022]
Abstract
Through a number of strategies nonribosomal peptide assembly lines give rise to a metabolic diversity not possible by ribosomal synthesis. One distinction within nonribosomal assembly is that products are elaborated on an enzyme-tethered substrate, and their release is enzyme catalysed. Reductive release by NAD(P)H-dependent catalysts is one observed nonribosomal termination and release strategy. Here we probed the selectivity of a terminal reductase domain by using a full-length heterologously expressed nonribosomal peptide synthetase for the dipeptide aureusimine and were able to generate 17 new analogues. Further, we generated an X-ray structure of aureusimine terminal reductase to gain insight into the structural details associated with this enzymatic domain.
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Affiliation(s)
- Morgan A Wyatt
- Michael G. Degroote Institute for Infectious Disease Research, McMaster University, 1200 Main St. W, Hamilton ON, L8N 3Z5, Canada
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236
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Wu Q, Wu Z, Qu X, Liu W. Insights into Pyrroindomycin Biosynthesis Reveal a Uniform Paradigm for Tetramate/Tetronate Formation. J Am Chem Soc 2012; 134:17342-5. [DOI: 10.1021/ja304829g] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Qiongqiong Wu
- State Key Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032,
China
| | - Zhuhua Wu
- State Key Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032,
China
| | - Xudong Qu
- State Key Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032,
China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032,
China
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237
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Haines BE, Steussy CN, Stauffacher CV, Wiest O. Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase. Biochemistry 2012; 51:7983-95. [PMID: 22971202 PMCID: PMC3522576 DOI: 10.1021/bi3008593] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HMG-CoA reductase catalyzes the four-electron reduction of HMG-CoA to mevalonate and is an enzyme of considerable biomedical relevance because of the impact of its statin inhibitors on public health. Although the reaction has been studied extensively using X-ray crystallography, there are surprisingly no computational studies that test the mechanistic hypotheses suggested for this complex reaction. Theozyme and quantum mechanical (QM)/molecular mechanical (MM) calculations up to the B3LYP/6-31g(d,p)//B3LYP/6-311++g(2d,2p) level of theory were employed to generate an atomistic description of the enzymatic reaction process and its energy profile. The models generated here predict that the catalytically important Glu83 is protonated prior to hydride transfer and that it acts as the general acid or base in the reaction. With Glu83 protonated, the activation energies calculated for the sequential hydride transfer reactions, 21.8 and 19.3 kcal/mol, are in qualitative agreement with the experimentally determined rate constant for the entire reaction (1 s(-1) to 1 min(-1)). When Glu83 is not protonated, the first hydride transfer reaction is predicted to be disfavored by >20 kcal/mol, and the activation energy is predicted to be higher by >10 kcal/mol. While not involved in the reaction as an acid or base, Lys267 is critical for stabilization of the transition state in forming an oxyanion hole with the protonated Glu83. Molecular dynamics simulations and MM/Poisson-Boltzmann surface area free energy calculations predict that the enzyme active site stabilizes the hemithioacetal intermediate better than the aldehyde intermediate. This suggests a mechanism in which cofactor exchange occurs before the breakdown of the hemithioacetal. Slowing the conversion to aldehyde would provide the enzyme with a mechanism to protect it from solvent and explain why the free aldehyde is not observed experimentally. Our results support the hypothesis that the pK(a) of an active site acidic group is modulated by the redox state of the cofactor. The oxidized cofactor and deprotonated Glu83 are closer in space after hydride transfer, indicating that indeed the cofactor may influence the pK(a) of Glu83 through an electrostatic interaction. The enzyme is able to catalyze the transfer of a hydride to the structurally and electronically distinct substrates by maintaining the general shape of the active site and adjusting the electrostatic environment through acid-base chemistry. Our results are in good agreement with the well-studied hydride transfer reactions catalyzed by liver alcohol dehydrogenase in calculated energy profile and reaction geometries despite different mechanistic functionalities.
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Affiliation(s)
- Brandon E. Haines
- Department of Chemistry and Biochemistry, Notre Dame University, Notre Dame, Indiana 46556
| | - C. Nicklaus Steussy
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | | | - Olaf Wiest
- Department of Chemistry and Biochemistry, Notre Dame University, Notre Dame, Indiana 46556
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238
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Belecki K, Townsend CA. Environmental control of the calicheamicin polyketide synthase leads to detection of a programmed octaketide and a proposal for enediyne biosynthesis. Angew Chem Int Ed Engl 2012; 51:11316-9. [PMID: 23042574 DOI: 10.1002/anie.201206462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Indexed: 11/09/2022]
Abstract
A light in the dark: the fermentation products of the polyketide synthase CalE8 (without its cognate thioesterase) were identified and gave some insight into the elusive early steps of calicheamicin biosynthesis. Fermentation in either the light or dark resulted in different proportions of a new octaketide and led to an updated mechanistic proposal.
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Affiliation(s)
- Katherine Belecki
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
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239
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Condurso HL, Bruner SD. Structure and noncanonical chemistry of nonribosomal peptide biosynthetic machinery. Nat Prod Rep 2012; 29:1099-110. [PMID: 22729219 PMCID: PMC3442147 DOI: 10.1039/c2np20023f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Structural biology has provided significant insights into the complex chemistry and macromolecular organization of nonribosomal peptide synthetases. In addition, novel pathways are continually described, expanding the knowledge of known biosynthetic chemistry.
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Affiliation(s)
- Heather L. Condurso
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA. Fax: 352 392 8758; Tel: 352 392 0525
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA. Fax: 352 392 8758; Tel: 352 392 0525
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240
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Yuzawa S, Kim W, Katz L, Keasling JD. Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli. Curr Opin Biotechnol 2012; 23:727-35. [DOI: 10.1016/j.copbio.2011.12.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 12/19/2011] [Accepted: 12/21/2011] [Indexed: 11/15/2022]
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241
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Wang WJ, Vogel H, Yao YJ, Ping L. The nonribosomal peptide and polyketide synthetic gene clusters in two strains of entomopathogenic fungi inCordyceps. FEMS Microbiol Lett 2012; 336:89-97. [DOI: 10.1111/j.1574-6968.2012.02658.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 06/01/2012] [Accepted: 08/07/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Heiko Vogel
- Department of Entomology; Max-Planck-Institute for Chemical Ecology; Jena; Germany
| | - Yi-Jian Yao
- State Key Laboratory of Mycology; Institute of Microbiology; Chinese Academy of Sciences; Beijing; China
| | - Liyan Ping
- Department of Bioorganic Chemistry; Max-Planck-Institute for Chemical Ecology; Jena; Germany
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242
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Shen Y, Huang H, Zhu L, Luo M, Chen D. Type II thioesterase gene (ECO-orf27) from Amycolatopsis orientalis influences production of the polyketide antibiotic, ECO-0501 (LW01). Biotechnol Lett 2012; 34:2087-91. [PMID: 22850790 DOI: 10.1007/s10529-012-1010-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 07/05/2012] [Indexed: 11/26/2022]
Abstract
ECO-orf27 associated with the cluster of ECO-0501 (LW01) from Amycolatopsis orientalis is deduced to encode a type II thioesterase. Disruption of ECO-orf27 reduced LW01 production by 95 %. Complementation of the disrupted mutant with intact ECO-orf27 restored the production of LW01 suggesting that ECO-orf27 is crucial for LW01 biosynthesis. ECO-TE I, the gene encoding type I thioesterase from LW01 polyketide synthases, cannot complement ECO-orf27 deficient mutant distinguishing ECO-orf27 from type I thioesterase gene. Type II thioesterase gene pikAV from Streptomyces venezuelae could complement ECO-orf27 in A. orientalis indicating that the two genes are equivalent in their function. Overexpression of ECO-orf27 resulted in a 20 % increase in LW01 production providing an alternative approach for yield improvement.
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Affiliation(s)
- Yang Shen
- School of Biotechnology, East China University of Science and Technology, Meilong Rd. 130#, Shanghai, People's Republic of China
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243
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Biggins JB, Ternei MA, Brady SF. Malleilactone, a polyketide synthase-derived virulence factor encoded by the cryptic secondary metabolome of Burkholderia pseudomallei group pathogens. J Am Chem Soc 2012; 134:13192-5. [PMID: 22765305 DOI: 10.1021/ja3052156] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sequenced bacterial genomes are routinely found to contain gene clusters that are predicted to encode metabolites not seen in fermentation-based studies. Pseudomallei group Burkholderia are emerging pathogens whose genomes are particularly rich in cryptic natural product biosynthetic gene clusters. We systematically probed the influence of the cryptic secondary metabolome on the virulence of these bacteria and found that disruption of the MAL gene cluster, which is natively silent in laboratory fermentation experiments and conserved across this group of pathogens, attenuates virulence in animal models. Using a promoter exchange strategy to activate the MAL cluster, we identified malleilactone, a polyketide synthase-derived cytotoxic siderophore encoded by this gene cluster. Small molecules targeting malleilactone biosynthesis either alone or in conjunction with antibiotics could prove useful as therapeutics to combat melioidosis and glanders.
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Affiliation(s)
- John B Biggins
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10068, USA
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244
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Jensen K, Niederkrüger H, Zimmermann K, Vagstad AL, Moldenhauer J, Brendel N, Frank S, Pöplau P, Kohlhaas C, Townsend CA, Oldiges M, Hertweck C, Piel J. Polyketide proofreading by an acyltransferase-like enzyme. ACTA ACUST UNITED AC 2012; 19:329-39. [PMID: 22444588 DOI: 10.1016/j.chembiol.2012.01.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 12/09/2011] [Accepted: 01/02/2012] [Indexed: 11/18/2022]
Abstract
Trans-acyltransferase polyketide synthases (trans-AT PKSs) are an important group of bacterial enzymes producing bioactive polyketides. One difference from textbook PKSs is the presence of one or more free-standing AT-like enzymes. While one homolog loads the PKS with malonyl units, the function of the second copy (AT2) was unknown. We studied the two ATs PedC and PedD involved in pederin biosynthesis in an uncultivated symbiont. PedD displayed malonyl- but not acetyltransferase activity toward various acyl carrier proteins (ACPs). In contrast, the AT2 PedC efficiently hydrolyzed acyl units bound to N-acetylcysteamine or ACP. It accepted substrates with various chain lengths and functionalizations but did not cleave malonyl-ACP. These data are consistent with the role of PedC in PKS proofreading, suggesting a similar function for other AT2 homologs and providing strategies for polyketide titer improvement and biosynthetic investigations.
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Affiliation(s)
- Katja Jensen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany
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245
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Vagstad AL, Bumpus SB, Belecki K, Kelleher NL, Townsend CA. Interrogation of global active site occupancy of a fungal iterative polyketide synthase reveals strategies for maintaining biosynthetic fidelity. J Am Chem Soc 2012; 134:6865-77. [PMID: 22452347 DOI: 10.1021/ja3016389] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nonreducing iterative polyketide synthases (NR-PKSs) are responsible for assembling the core of fungal aromatic natural products with diverse biological properties. Despite recent advances in the field, many mechanistic details of polyketide assembly by these megasynthases remain unknown. To expand our understanding of substrate loading, polyketide elongation, cyclization, and product release, active site occupancy and product output were explored by Fourier transform mass spectrometry using the norsolorinic acid anthrone-producing polyketide synthase, PksA, from the aflatoxin biosynthetic pathway in Aspergillus parasiticus. Here we report the simultaneous observation of covalent intermediates from all catalytic domains of PksA from in vitro reconstitution reactions. The data provide snapshots of iterative catalysis and reveal an underappreciated editing function for the C-terminal thioesterase domain beyond its recently established synthetic role in Claisen/Dieckmann cyclization and product release. The specificity of thioesterase catalyzed hydrolysis was explored using biosynthetically relevant protein-bound and small molecule acyl substrates and demonstrated activity against hexanoyl and acetyl, but not malonyl. Processivity of polyketide extension was supported by the inability of a nonhydrolyzable malonyl analog to trap products of intermediate chain lengths and by the detection of only fully extended species observed covalently bound to, and as the predominant products released by, PksA. High occupancy of the malonyl transacylase domain and fast relative rate of malonyl transfer compared to starter unit transfer indicate that rapid loading of extension units onto the carrier domain facilitates efficient chain extension in a manner kinetically favorable to ultimate product formation.
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Affiliation(s)
- Anna L Vagstad
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland, USA
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246
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Biosynthesis of fusarubins accounts for pigmentation of Fusarium fujikuroi perithecia. Appl Environ Microbiol 2012; 78:4468-80. [PMID: 22492438 DOI: 10.1128/aem.00823-12] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Fusarium fujikuroi produces a variety of secondary metabolites, of which polyketides form the most diverse group. Among these are the highly pigmented naphthoquinones, which have been shown to possess different functional properties for the fungus. A group of naphthoquinones, polyketides related to fusarubin, were identified in Fusarium spp. more than 60 years ago, but neither the genes responsible for their formation nor their biological function has been discovered to date. In addition, although it is known that the sexual fruiting bodies in which the progeny of the fungus develops are darkly colored by a polyketide synthase (PKS)-derived pigment, the structure of this pigment has never been elucidated. Here we present data that link the fusarubin-type polyketides to a defined gene cluster, which we designate fsr, and demonstrate that the fusarubins are the pigments responsible for the coloration of the perithecia. We studied their regulation and the function of the single genes within the cluster by a combination of gene replacements and overexpression of the PKS-encoding gene, and we present a model for the biosynthetic pathway of the fusarubins based on these data.
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247
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Hansen FT, Sørensen JL, Giese H, Sondergaard TE, Frandsen RJ. Quick guide to polyketide synthase and nonribosomal synthetase genes in Fusarium. Int J Food Microbiol 2012; 155:128-36. [DOI: 10.1016/j.ijfoodmicro.2012.01.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/16/2012] [Accepted: 01/23/2012] [Indexed: 11/25/2022]
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248
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Nonprocessive [2 + 2]e- off-loading reductase domains from mycobacterial nonribosomal peptide synthetases. Proc Natl Acad Sci U S A 2012; 109:5681-6. [PMID: 22451903 DOI: 10.1073/pnas.1118680109] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In mycobacteria, polyketide synthases and nonribosomal peptide synthetases (NRPSs) produce complex lipidic metabolites by using a thio-template mechanism of catalysis. In this study, we demonstrate that off-loading reductase (R) domain of mycobacterial NRPSs performs two consecutive [2 + 2]e(-) reductions to release thioester-bound lipopeptides as corresponding alcohols, using a nonprocessive mechanism of catalysis. The first crystal structure of an R domain from Mycobacterium tuberculosis NRPS provides strong support to this mechanistic model and suggests that the displacement of intermediate would be required for cofactor recycling. We show that 4e(-) reductases produce alcohols through a committed aldehyde intermediate, and the reduction of this intermediate is at least 10 times more efficient than the thioester-substrate. Structural and biochemical studies also provide evidence for the conformational changes associated with the reductive cycle. Further, we show that the large substrate-binding pocket with a hydrophobic platform accounts for the remarkable substrate promiscuity of these domains. Our studies present an elegant example of the recruitment of a canonical short-chain dehydrogenase/reductase family member as an off-loading domain in the context of assembly-line enzymology.
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249
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Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A. The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics 2012; 13:112. [PMID: 22443545 PMCID: PMC3364876 DOI: 10.1186/1471-2164-13-112] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 03/23/2012] [Indexed: 11/16/2022] Open
Abstract
Background Actinoplanes sp. SE50/110 is known as the wild type producer of the alpha-glucosidase inhibitor acarbose, a potent drug used worldwide in the treatment of type-2 diabetes mellitus. As the incidence of diabetes is rapidly rising worldwide, an ever increasing demand for diabetes drugs, such as acarbose, needs to be anticipated. Consequently, derived Actinoplanes strains with increased acarbose yields are being used in large scale industrial batch fermentation since 1990 and were continuously optimized by conventional mutagenesis and screening experiments. This strategy reached its limits and is generally superseded by modern genetic engineering approaches. As a prerequisite for targeted genetic modifications, the complete genome sequence of the organism has to be known. Results Here, we present the complete genome sequence of Actinoplanes sp. SE50/110 [GenBank:CP003170], the first publicly available genome of the genus Actinoplanes, comprising various producers of pharmaceutically and economically important secondary metabolites. The genome features a high mean G + C content of 71.32% and consists of one circular chromosome with a size of 9,239,851 bp hosting 8,270 predicted protein coding sequences. Phylogenetic analysis of the core genome revealed a rather distant relation to other sequenced species of the family Micromonosporaceae whereas Actinoplanes utahensis was found to be the closest species based on 16S rRNA gene sequence comparison. Besides the already published acarbose biosynthetic gene cluster sequence, several new non-ribosomal peptide synthetase-, polyketide synthase- and hybrid-clusters were identified on the Actinoplanes genome. Another key feature of the genome represents the discovery of a functional actinomycete integrative and conjugative element. Conclusions The complete genome sequence of Actinoplanes sp. SE50/110 marks an important step towards the rational genetic optimization of the acarbose production. In this regard, the identified actinomycete integrative and conjugative element could play a central role by providing the basis for the development of a genetic transformation system for Actinoplanes sp. SE50/110 and other Actinoplanes spp. Furthermore, the identified non-ribosomal peptide synthetase- and polyketide synthase-clusters potentially encode new antibiotics and/or other bioactive compounds, which might be of pharmacologic interest.
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Affiliation(s)
- Patrick Schwientek
- Senior research group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Germany
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250
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Klejnstrup ML, Frandsen RJN, Holm DK, Nielsen MT, Mortensen UH, Larsen TO, Nielsen JB. Genetics of Polyketide Metabolism in Aspergillus nidulans. Metabolites 2012; 2:100-33. [PMID: 24957370 PMCID: PMC3901194 DOI: 10.3390/metabo2010100] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/23/2011] [Accepted: 01/17/2012] [Indexed: 12/12/2022] Open
Abstract
Secondary metabolites are small molecules that show large structural diversity and a broad range of bioactivities. Some metabolites are attractive as drugs or pigments while others act as harmful mycotoxins. Filamentous fungi have the capacity to produce a wide array of secondary metabolites including polyketides. The majority of genes required for production of these metabolites are mostly organized in gene clusters, which often are silent or barely expressed under laboratory conditions, making discovery and analysis difficult. Fortunately, the genome sequences of several filamentous fungi are publicly available, greatly facilitating the establishment of links between genes and metabolites. This review covers the attempts being made to trigger the activation of polyketide metabolism in the fungal model organism Aspergillus nidulans. Moreover, it will provide an overview of the pathways where ten polyketide synthase genes have been coupled to polyketide products. Therefore, the proposed biosynthesis of the following metabolites will be presented; naphthopyrone, sterigmatocystin, aspyridones, emericellamides, asperthecin, asperfuranone, monodictyphenone/emodin, orsellinic acid, and the austinols.
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Affiliation(s)
- Marie L Klejnstrup
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B221, DK-2800 Kgs. Lyngby, Denmark.
| | - Rasmus J N Frandsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B223, DK-2800 Kgs. Lyngby, Denmark.
| | - Dorte K Holm
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B223, DK-2800 Kgs. Lyngby, Denmark.
| | - Morten T Nielsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B223, DK-2800 Kgs. Lyngby, Denmark.
| | - Uffe H Mortensen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B223, DK-2800 Kgs. Lyngby, Denmark.
| | - Thomas O Larsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B221, DK-2800 Kgs. Lyngby, Denmark.
| | - Jakob B Nielsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads B223, DK-2800 Kgs. Lyngby, Denmark.
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