1
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Heard SC, Winter JM. Structural, biochemical and bioinformatic analyses of nonribosomal peptide synthetase adenylation domains. Nat Prod Rep 2024; 41:1180-1205. [PMID: 38488017 PMCID: PMC11253843 DOI: 10.1039/d3np00064h] [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] [Received: 12/12/2023] [Indexed: 07/18/2024]
Abstract
Covering: 1997 to July 2023The adenylation reaction has been a subject of scientific intrigue since it was first recognized as essential to many biological processes, including the homeostasis and pathogenicity of some bacteria and the activation of amino acids for protein synthesis in mammals. Several foundational studies on adenylation (A) domains have facilitated an improved understanding of their molecular structures and biochemical properties, in particular work on nonribosomal peptide synthetases (NRPSs). In NRPS pathways, A domains activate their respective acyl substrates for incorporation into a growing peptidyl chain, and many nonribosomal peptides are bioactive. From a natural product drug discovery perspective, improving existing bioinformatics platforms to predict unique NRPS products more accurately from genomic data is desirable. Here, we summarize characterization efforts of A domains primarily from NRPS pathways from July 1997 up to July 2023, covering protein structure elucidation, in vitro assay development, and in silico tools for improved predictions.
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Affiliation(s)
- Stephanie C Heard
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA.
| | - Jaclyn M Winter
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA.
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2
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Cheng Y, Yi X, Zhang Y, He Q, Chen D, Cao W, Fang P, Liu W. Oxidase Heterotetramer Completes 1-Azabicyclo[3.1.0]hexane Formation with the Association of a Nonribosomal Peptide Synthetase. J Am Chem Soc 2023; 145:8896-8907. [PMID: 37043819 DOI: 10.1021/jacs.2c12507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Ficellomycin, azinomycins, and vazabitide A are nonribosomal peptide natural products characterized by an amino acid unit that contains a similar 1-azabicyclo[3.1.0]hexane (ABCH) pharmacophore. This unit is derived from diamino-dihydroxy-heptanic acid (DADH); however, the process through which linear DADH is cyclized to furnish an ABCH ring system remains poorly understood. Based on the reconstitution of the route of the ABCH-containing unit by blending genes/enzymes involved in the biosynthesis of ficellomycin and azinomycins, we report that ABCH formation is completed by an oxidase heterotetramer with the association of a nonribosomal peptide synthetase (NRPS). The DADH precursor was prepared in Escherichia coli to produce a conjugate subjected to in vitro enzymatic hydrolysis for offloading from an amino-group carrier protein. To furnish an aziridine ring, DADH was processed by C7-hydroxyl sulfonation and sulfate elimination-coupled cyclization. Further cyclization leading to an azabicyclic hexane pharmacophore was proved to occur in the NRPS, where the oxidase heterotetramer functions in trans and catalyzes α,β-dehydrogenation to initiate the formation of a fused five-membered nitrogen heterocycle. The identity of ABCH was validated by utilization of the resultant ABCH-containing unit in the total biosynthesis of ficellomycin. Biochemical characterization, crystal structure, and site-specific mutagenesis rationalize the catalytic mechanism of the unusual oxidase heterotetramer.
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Affiliation(s)
- Yiyuan Cheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xuan Yi
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yan Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qingli He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Dandan Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Weiguo Cao
- Department of Chemistry, Shanghai University, 99 Shangda Rd, Baoshan, Shanghai 200444, China
| | - Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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3
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Guo S, Sang Y, Zheng C, Xue XS, Tang Z, Liu W. Enzymatic α-Ketothioester Decarbonylation Occurs in the Assembly Line of Barbamide for Skeleton Editing. J Am Chem Soc 2023; 145:5017-5028. [PMID: 36821526 DOI: 10.1021/jacs.2c10277] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The decarbonylation reaction has been developed significantly in organic chemistry as an effective approach to various synthetic applications, but enzymatic precedents for this reaction are rare. Based on investigations into the hybrid nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) assembly line of barbamide, we report an on-line α-ketothioester decarbonylation reaction that leads to one-carbon truncation of the elongating skeleton. This enzymatic editing reaction occurs in the first round of lipopeptide extension and modification involving the multienzymes BarE and BarF, which successively house an NRPS module to initiate the biosynthesis and a PKS module to catalyze the first round of chain extension. Starting with processing a leucine-derived α-ketoacyl starter, the ketosynthase domain in BarE displays an unusual dual activity that results in net one-carbon chain elongation. It extrudes carbon monoxide from α-keto-isocaproyl thioester and then mediates decarboxylative condenses of the resultant isovaleryl thioester with malonyl thioester to form a diketide intermediate, followed by BarF-based O-methylation to stabilize the enol form of the β-carbonyl and afford an unusual E-double bond. Biochemical characterization, chemical synthesis, computational analysis, and the experimental outcome of site-directed mutagenesis illustrate the extraordinary catalytic capability of this ketosynthase domain. This work furthers the appreciation of assembly line chemistry and opens the door to new approaches for skeleton editing/engineering of related molecules using synthetic biology approaches.
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Affiliation(s)
- Shengjie Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yueqian Sang
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Chao Zheng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Song Xue
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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4
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Wang S, Cheng Y, Wang X, Yang Q, Liu W. Tracing of Acyl Carrier Protein-channeled Mitomycin Intermediates in Streptomyces caespitosus Facilitates Characterization of the Biosynthetic Steps for AHBA-GlcN Formation and Processing. J Am Chem Soc 2022; 144:14945-14956. [PMID: 35943208 DOI: 10.1021/jacs.2c06969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mitomycins are a family of naturally occurring, potent alkylating agents in which the C member has been clinically used for cancer chemotherapy for over 5 decades. In Streptomyces caespitosus, mitomycins are derived from an N-glycoside composed of a 3-amino-5-hydroxybenzoic acid (AHBA) unit and a d-glucosamine (GlcN) unit; however, how this N-glycoside is formed and rearranged to a mitosane, for example, the compact polycyclic ring system of mitomycin C, remains elusive. Benefiting from the development of a method used to trace the mitomycin intermediates that accumulate on an acyl carrier protein (ACP), we here dissect the enzymatic steps for AHBA-GlcN formation and processing to underlie the mitosane structure. Following the N-glycosylation of AHBA with activated N-acetyl-GlcN, deacetylation occurs on ACP to provide AHBA-GlcN. Then, the sugar portion of this N-glycoside is transformed into a linear aminodiol that terminates with an epoxyethane, yielding an ACP-channeled intermediate that is ready for mitosane formation through crosslinking between the AHBA and linearized sugar units. This transformation is unusual and relies on the functional association of a dihydronicotinamide adenine dinucleotide (phosphate)-dependent protein with a radical S-adenosyl-l-methionine protein. Characterization of these ACP-based enzymatic steps for AHBA-GlcN formation and processing sheds light on the poorly understood biosynthetic pathway of mitomycins.
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Affiliation(s)
- Sili Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yiyuan Cheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xiaofeng Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
| | - Qian Yang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of 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, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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5
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Washburn LA, Nepal KK, Watanabe CMH. A Capture Strategy for the Identification of Thio-Templated Metabolites. ACS Chem Biol 2021; 16:1737-1744. [PMID: 34423966 DOI: 10.1021/acschembio.1c00437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonribosomal peptide synthetase and polyketide synthase systems are home to complex enzymology and produce compounds of great therapeutic value. Despite this, they have continued to be difficult to characterize due to their substrates remaining enzyme-bound by a thioester bond. Here, we have developed a strategy to directly trap and characterize the thioester-bound enzyme intermediates and applied the strategy to the azinomycin biosynthetic pathway. The approach was initially applied in vitro to evaluate its efficacy and subsequently moved to an in situ system, where a protein of interest was isolated from the native organism to avoid needing to supply substrates. When the nonribosomal peptide synthetase AziA3 was isolated from Streptomyces sahachiroi, the capture strategy revealed AziA3 functions in the late stages of epoxide moiety formation of the azinomycins. The strategy was further validated in vitro with a nonribosomal peptide synthetase involved in colibactin biosynthesis. In the long term, this method will be utilized to characterize thioester-bound metabolites within not only the azinomycin biosynthetic pathway but also other cryptic metabolite pathways.
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Affiliation(s)
- Lauren A. Washburn
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Keshav K. Nepal
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Coran M. H. Watanabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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6
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Pang B, Liao R, Tang Z, Guo S, Wu Z, Liu W. Caerulomycin and collismycin antibiotics share a trans-acting flavoprotein-dependent assembly line for 2,2'-bipyridine formation. Nat Commun 2021; 12:3124. [PMID: 34035275 PMCID: PMC8149447 DOI: 10.1038/s41467-021-23475-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
Linear nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) template the modular biosynthesis of numerous nonribosomal peptides, polyketides and their hybrids through assembly line chemistry. This chemistry can be complex and highly varied, and thus challenges our understanding in NRPS and PKS-programmed, diverse biosynthetic processes using amino acid and carboxylate building blocks. Here, we report that caerulomycin and collismycin peptide-polyketide hybrid antibiotics share an assembly line that involves unusual NRPS activity to engage a trans-acting flavoprotein in C-C bond formation and heterocyclization during 2,2'-bipyridine formation. Simultaneously, this assembly line provides dethiolated and thiolated 2,2'-bipyridine intermediates through differential treatment of the sulfhydryl group arising from L-cysteine incorporation. Subsequent L-leucine extension, which does not contribute any atoms to either caerulomycins or collismycins, plays a key role in sulfur fate determination by selectively advancing one of the two 2,2'-bipyridine intermediates down a path to the final products with or without sulfur decoration. These findings further the appreciation of assembly line chemistry and will facilitate the development of related molecules using synthetic biology approaches.
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Affiliation(s)
- Bo Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Rijing Liao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Shengjie Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Zhuhua Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. .,Huzhou Center of Bio-Synthetic Innovation, Huzhou, China.
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7
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Ishikawa F, Tanabe G, Kakeya H. Activity-Based Protein Profiling of Non-ribosomal Peptide Synthetases. Curr Top Microbiol Immunol 2018; 420:321-349. [PMID: 30178264 DOI: 10.1007/82_2018_133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-ribosomal peptide (NRP) natural products are one of the most promising resources for drug discovery and development because of their wide-ranging of therapeutic potential, and their behavior as virulence factors and signaling molecules. The NRPs are biosynthesized independently of the ribosome by enzyme assembly lines known as the non-ribosomal peptide synthetase (NRPS) machinery. Genetic, biochemical, and bioinformatics analyses have provided a detailed understanding of the mechanism of NRPS catalysis. However, proteomic techniques for natural product biosynthesis remain a developing field. New strategies are needed to investigate the proteomes of diverse producer organisms and directly analyze the endogenous NRPS machinery. Advanced platforms should verify protein expression, protein folding, and activities and also enable the profiling of the NRPS machinery in biological samples from wild-type, heterologous, and engineered bacterial systems. Here, we focus on activity-based protein profiling strategies that have been recently developed for studies aimed at visualizing and monitoring the NRPS machinery and also for rapid labeling, identification, and biochemical analysis of NRPS enzyme family members as required for proteomic chemistry in natural product sciences.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan.
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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8
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Havemann J, Yurkovich ME, Jenkins R, Harringer S, Tao W, Wen S, Sun Y, Leadlay PF, Tosin M. Chemical probing of thiotetronate bio-assembly. Chem Commun (Camb) 2017; 53:1912-1915. [DOI: 10.1039/c6cc09933e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemical ‘chain termination’ probes were utilised for the investigation of thiotetronate antibiotic biosynthesis in the filamentous bacteria Lentzea sp. and Streptomyces thiolactonus NRRL 15439.
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Affiliation(s)
| | | | | | | | - Weixin Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University)
- Ministry of Education
- Wuhan University School of Pharmaceutical Sciences
- Wuhan 430071
- People's Republic of China
| | - Shishi Wen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University)
- Ministry of Education
- Wuhan University School of Pharmaceutical Sciences
- Wuhan 430071
- People's Republic of China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University)
- Ministry of Education
- Wuhan University School of Pharmaceutical Sciences
- Wuhan 430071
- People's Republic of China
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9
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Noga MJ, Cerri M, Imholz N, Tulinski P, Şahin E, Bokinsky G. Mass-Spectrometry-Based Quantification of Protein-Bound Fatty Acid Synthesis Intermediates from Escherichia coli. J Proteome Res 2016; 15:3617-3623. [PMID: 27595277 DOI: 10.1021/acs.jproteome.6b00405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The production of fatty acids from simple nutrients occurs via a complex biosynthetic pathway with dozens of intermediate compounds and multiple branch points. Despite its importance for microbial physiology and biotechnology, critical aspects of fatty acid biosynthesis, especially dynamics of in vivo regulation, remain poorly characterized. We have developed a liquid chromatography/mass spectroscopy (LC-MS) method for relative quantification of fatty acid synthesis intermediates in Escherichia coli, a model organism for studies of fatty acid metabolism. The acyl carrier protein, a vehicle for the substrates and intermediates of fatty acid synthesis, is extracted from E. coli, proteolytically digested, resolved using reverse-phase LC, and detected using electrospray ionization coupled with a tandem MS. Our method reliably resolves 21 intermediates of fatty acid synthesis, with an average relative standard deviation in ratios of individual acyl-ACP species to total ACP concentrations of 20%. We demonstrate that fast sampling and quenching of cells is essential to accurately characterize intracellular concentrations of ACP species. We apply our method to examine the rapid response of fatty acid metabolism to the antibiotic cerulenin. We anticipate that our method will enable the characterization of in vivo regulation and kinetics of microbial fatty acid synthesis at unprecedented detail and will improve integration of fatty acid synthesis into models of microbial metabolism.
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Affiliation(s)
- Marek J Noga
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Mattia Cerri
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Nicole Imholz
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Pawel Tulinski
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Enes Şahin
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Gregory Bokinsky
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
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10
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Wilkening I, Gazzola S, Riva E, Parascandolo JS, Song L, Tosin M. Second-generation probes for biosynthetic intermediate capture: towards a comprehensive profiling of polyketide assembly. Chem Commun (Camb) 2016; 52:10392-5. [PMID: 27481638 PMCID: PMC5050551 DOI: 10.1039/c6cc04681a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/28/2016] [Indexed: 12/12/2022]
Abstract
Malonyl carba(dethia) N-decanoyl cysteamine methyl esters and novel acetoxymethyl esters were utilised as second-generation probes for polyketide intermediate capture. The use of these tools in vivo led to the characterisation of an almost complete set of biosynthetic intermediates from a modular assembly line, providing a first kinetic overview of intermediate processing leading to complex natural product formation.
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Affiliation(s)
- Ina Wilkening
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Silvia Gazzola
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK. and Dipartimento di Scienza ed Alta Tecnologia, Universita' dell'Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Elena Riva
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | | | - Lijiang Song
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
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11
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Shakya G, Rivera H, Lee DJ, Jaremko MJ, La Clair JJ, Fox DT, Haushalter RW, Schaub AJ, Bruegger J, Barajas JF, White AR, Kaur P, Gwozdziowski ER, Wong F, Tsai SC, Burkart MD. Modeling linear and cyclic PKS intermediates through atom replacement. J Am Chem Soc 2014; 136:16792-9. [PMID: 25406716 PMCID: PMC4277753 DOI: 10.1021/ja5064857] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 11/30/2022]
Abstract
The mechanistic details of many polyketide synthases (PKSs) remain elusive due to the instability of transient intermediates that are not accessible via conventional methods. Here we report an atom replacement strategy that enables the rapid preparation of polyketone surrogates by selective atom replacement, thereby providing key substrate mimetics for detailed mechanistic evaluations. Polyketone mimetics are positioned on the actinorhodin acyl carrier protein (actACP) to probe the underpinnings of substrate association upon nascent chain elongation and processivity. Protein NMR is used to visualize substrate interaction with the actACP, where a tetraketide substrate is shown not to bind within the protein, while heptaketide and octaketide substrates show strong association between helix II and IV. To examine the later cyclization stages, we extended this strategy to prepare stabilized cyclic intermediates and evaluate their binding by the actACP. Elongated monocyclic mimics show much longer residence time within actACP than shortened analogs. Taken together, these observations suggest ACP-substrate association occurs both before and after ketoreductase action upon the fully elongated polyketone, indicating a key role played by the ACP within PKS timing and processivity. These atom replacement mimetics offer new tools to study protein and substrate interactions and are applicable to a wide variety of PKSs.
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Affiliation(s)
- Gaurav Shakya
- Departments
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, California 92697, United States
| | - Heriberto Rivera
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - D. John Lee
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Matt J. Jaremko
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - James J. La Clair
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Daniel T. Fox
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Robert W. Haushalter
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Andrew J. Schaub
- Departments
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, California 92697, United States
| | - Joel Bruegger
- Departments
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, California 92697, United States
| | - Jesus F. Barajas
- Departments
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, California 92697, United States
| | - Alexander R. White
- Departments
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, California 92697, United States
| | - Parminder Kaur
- Departments
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, California 92697, United States
| | - Emily R. Gwozdziowski
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Fiona Wong
- Departments
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, California 92697, United States
| | - Shiou-Chuan Tsai
- Departments
of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical
Sciences, University of California, Irvine, California 92697, United States
| | - Michael D. Burkart
- Department
of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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12
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Poust S, Hagen A, Katz L, Keasling JD. Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform. Curr Opin Biotechnol 2014; 30:32-9. [DOI: 10.1016/j.copbio.2014.04.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 11/27/2022]
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13
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Poust S, Yoon I, Adams PD, Katz L, Petzold CJ, Keasling JD. Understanding the role of histidine in the GHSxG acyltransferase active site motif: evidence for histidine stabilization of the malonyl-enzyme intermediate. PLoS One 2014; 9:e109421. [PMID: 25286165 PMCID: PMC4186864 DOI: 10.1371/journal.pone.0109421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/30/2014] [Indexed: 11/18/2022] Open
Abstract
Acyltransferases determine which extender units are incorporated into polyketide and fatty acid products. The ping-pong acyltransferase mechanism utilizes a serine in a conserved GHSxG motif. However, the role of the conserved histidine in this motif is poorly understood. We observed that a histidine to alanine mutation (H640A) in the GHSxG motif of the malonyl-CoA specific yersiniabactin acyltransferase results in an approximately seven-fold higher hydrolysis rate over the wildtype enzyme, while retaining transacylation activity. We propose two possibilities for the reduction in hydrolysis rate: either H640 structurally stabilizes the protein by hydrogen bonding with a conserved asparagine in the ferredoxin-like subdomain of the protein, or a water-mediated hydrogen bond between H640 and the malonyl moiety stabilizes the malonyl-O-AT ester intermediate.
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Affiliation(s)
- Sean Poust
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
| | - Isu Yoon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Bioscience division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Leonard Katz
- Synthetic Biology Engineering Research Center, Emeryville, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Bioscience division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jay D. Keasling
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
- QB3 Institute, University of California, Berkeley, California, United States of America
- Synthetic Biology Engineering Research Center, Emeryville, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Bioscience division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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14
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Expedient preparative isolation and tandem mass spectrometric characterization of C-seco triterpenoids from Neem oil. J Chromatogr A 2014; 1366:1-14. [DOI: 10.1016/j.chroma.2014.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/02/2014] [Accepted: 09/04/2014] [Indexed: 11/18/2022]
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15
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Wills RH, Tosin M, O'Connor PB. Structural characterization of polyketides using high mass accuracy tandem mass spectrometry. Anal Chem 2012; 84:8863-70. [PMID: 22985101 DOI: 10.1021/ac3022778] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tandem mass spectrometry techniques electron-induced dissociation (EID) and collision-activated dissociation (CAD) have been compared as tools for providing detailed structural information of polyketides. Polyketides are an important class of natural products that account for a significant proportion of the drugs currently in clinical use. Three polyketide natural products, namely erythromycin A, lasalocid A, and iso-lasalocid A, were subjected to both CAD and EID, and their fragment ions were assigned with sub-part-per-million accuracy. The number of fragment ions detected through EID was much greater than for CAD, leading to a greater amount of structural information obtained for each polyketide, albeit with a decreased signal-to-noise ratio. The effect of different bound cations on the fragment pattern of the isomers lasalocid A and iso-lasalocid A was studied, with CAD and EID performed on the [M + H](+), [M + Na](+), [M + Li](+), and [M + NH(4)](+) precursor ions. The lithiated species were found to produce the greatest degree of fragmentation and enabled detailed structural information on the isomers to be obtained. Multistage mass spectrometry (MS(3)) experiments, combining CAD and EID, could also be performed on the lithiated species, generating new fragment information which enables the two isomers to be distinguished. Combining CAD and EID for the structural characterization of polyketides will therefore be a useful tool for identifying and characterizing unknown polyketides and their biosynthetic intermediates.
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Affiliation(s)
- Rebecca H Wills
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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16
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Crosby J, Crump MP. The structural role of the carrier protein--active controller or passive carrier. Nat Prod Rep 2012; 29:1111-37. [PMID: 22930263 DOI: 10.1039/c2np20062g] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Common to all FASs, PKSs and NRPSs is a remarkable component, the acyl or peptidyl carrier protein (A/PCP). These take the form of small individual proteins in type II systems or discrete folded domains in the multi-domain type I systems and are characterized by a fold consisting of three major α-helices and between 60-100 amino acids. This protein is central to these biosynthetic systems and it must bind and transport a wide variety of functionalized ligands as well as mediate numerous protein-protein interactions, all of which contribute to efficient enzyme turnover. This review covers the structural and biochemical characterization of carrier proteins, as well as assessing their interactions with different ligands, and other synthase components. Finally, their role as an emerging tool in biotechnology is discussed.
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Affiliation(s)
- John Crosby
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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17
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18
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Hollenhorst MA, Bumpus SB, Matthews ML, Bollinger JM, Kelleher NL, Walsh CT. The nonribosomal peptide synthetase enzyme DdaD tethers N(β)-fumaramoyl-l-2,3-diaminopropionate for Fe(II)/α-ketoglutarate-dependent epoxidation by DdaC during dapdiamide antibiotic biosynthesis. J Am Chem Soc 2011; 132:15773-81. [PMID: 20945916 DOI: 10.1021/ja1072367] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The gene cluster from Pantoea agglomerans responsible for biosynthesis of the dapdiamide antibiotics encodes an adenylation-thiolation didomain protein, DdaD, and an Fe(II)/α-ketoglutarate-dependent dioxygenase homologue, DdaC. Here we show that DdaD, a nonribosomal peptide synthetase module, activates and sequesters N(β)-fumaramoyl-l-2,3-diaminopropionate as a covalently tethered thioester for subsequent oxidative modification of the fumaramoyl group. DdaC catalyzes Fe(II)- and α-ketoglutarate-dependent epoxidation of the covalently bound N(β)-fumaramoyl-l-2,3-diaminopropionyl-S-DdaD species to generate N(β)-epoxysuccinamoyl-DAP (DAP = 2,3-diaminopropionate) in thioester linkage to DdaD. After hydrolytic release, N(β)-epoxysuccinamoyl-DAP can be ligated to l-valine by the ATP-dependent ligase DdaF to form the natural antibiotic N(β)-epoxysuccinamoyl-DAP-Val.
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Affiliation(s)
- Marie A Hollenhorst
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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19
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Süssmuth R, Müller J, von Döhren H, Molnár I. Fungal cyclooligomerdepsipeptides: From classical biochemistry to combinatorial biosynthesis. Nat Prod Rep 2011; 28:99-124. [DOI: 10.1039/c001463j] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Meehan MJ, Xie X, Zhao X, Xu W, Tang Y, Dorrestein PC. FT-ICR-MS characterization of intermediates in the biosynthesis of the α-methylbutyrate side chain of lovastatin by the 277 kDa polyketide synthase LovF. Biochemistry 2010; 50:287-99. [PMID: 21069965 DOI: 10.1021/bi1014776] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There are very few fungal polyketide synthases that have been characterized by mass spectrometry. In this paper we describe the in vitro reconstitution and FT-ICR-MS verification of the full activity of an intact 277 kDa fungal polyketide synthase LovF of the lovastatin biosynthetic pathway. We report here both the verification of the reconstitution of fully functional holo-LovF by using (13)C-labeled malonyl-CoA to form α-methylbutyrate functionality and also detection of five predicted intermediates covalently bound to the 4'-phosphopantetheine at the acyl carrier protein (ACP) active site utilizing the phosphopantetheine ejection assay and high-resolution mass spectrometry. Under in vitro conditions, the diketide acetoacetyl intermediate did not accumulate on the ACP active site of holo-LovF following incubation with malonyl-CoA substrate. We found that incubation of holo-LovF with acetoacetyl-CoA served as an effective means of loading the diketide intermediate onto the ACP active site of LovF. Our results demonstrate that subsequent α-methylation of the acetoacetyl intermediate stabilizes the intermediate onto the ACP active site and facilitates the formation and mass spectrometric detection of additional intermediates en route to the formation of α-methylbutyrate.
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Affiliation(s)
- Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 92093, United States
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21
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Proteomic analysis of polyketide and nonribosomal peptide biosynthesis. Curr Opin Chem Biol 2010; 15:48-56. [PMID: 21087894 DOI: 10.1016/j.cbpa.2010.10.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 10/15/2010] [Indexed: 01/18/2023]
Abstract
Polyketides and non-ribosomal peptides are in a class of natural products important both as drug sources and as dangerous toxins and virulence factors. While studies over the last two decades have provided substantial characterization of the modular synthases that produce these compounds at the genetic level, their understanding at the protein level is much less understood. New proteomic platforms called an orthogonal active site identification system (OASIS) and proteomic interrogation of secondary metabolism (PrISM) have been developed to identify and quantify natural product synthase enzymes. Reviewed here, these tools offer the means to discover and analyze modular synthetic pathways that are limited by genetic techniques, opening the tools of contemporary proteomics to natural product sciences.
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22
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Tosin M, Betancor L, Stephens E, Ariel Li WM, Spencer JB, Leadlay PF. Synthetic Chain Terminators Off-Load Intermediates from a Type I Polyketide Synthase. Chembiochem 2010; 11:539-46. [DOI: 10.1002/cbic.200900772] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Hong H, Leadlay PF, Staunton J. The changing patterns of covalent active site occupancy during catalysis on a modular polyketide synthase multienzyme revealed by ion-trap mass spectrometry. FEBS J 2009; 276:7057-69. [PMID: 19860832 DOI: 10.1111/j.1742-4658.2009.07418.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A catalytically competent, homodimeric diketide synthase comprising the first extension module of the erythromycin polyketide synthase was analysed using MS, after limited proteolysis to release functional domains, to determine the pattern of covalent attachment of substrates and intermediates to active sites during catalysis. Using the natural substrates, the acyltransferase and acylcarrier protein of the loading module were found to be heavily loaded with propionyl starter groups, while the ketosynthase was fully propionylated. The acylcarrier protein of the extension module was partly occupied by the product diketide, and the adjacent chain-releasing thioesterase domain was vacant, implying that the rate-limiting step is transfer of the diketide from the acylcarrier protein to the thioesterase domain. The data suggest an attractive model for preventing iterative chain extension by efficient repriming of the ketosynthase domain after condensation. Use of the alternative starter unit valeryl-CoA produced an altered pattern, in which a significant proportion of the extension acylcarrier protein was loaded with methylmalonate, not diketide, consistent with the condensation step having become an additional slow step. Strikingly, when NADPH was omitted, the extension acylcarrier protein contained methylmalonate and none of the expected keto diketide, in contrast to results obtained previously by mixing individual recombinant domains, showing the importance of also studying intact modules. The detailed patterns of loading of the extension acylcarrier protein (of which there are two in the homodimer) also provided the first evidence for simultaneous loading of both acylcarrier proteins and for the coordination of timing between the two active centres for chain extension.
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Affiliation(s)
- Hui Hong
- Department of Chemistry, University of Cambridge, UK.
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24
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Kopriva I, Jerić I. Multi-component analysis: blind extraction of pure components mass spectra using sparse component analysis. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:1378-1388. [PMID: 19670286 DOI: 10.1002/jms.1627] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The paper presents sparse component analysis (SCA)-based blind decomposition of the mixtures of mass spectra into pure components, wherein the number of mixtures is less than number of pure components. Standard solutions of the related blind source separation (BSS) problem that are published in the open literature require the number of mixtures to be greater than or equal to the unknown number of pure components. Specifically, we have demonstrated experimentally the capability of the SCA to blindly extract five pure components mass spectra from two mixtures only. Two approaches to SCA are tested: the first one based on l(1) norm minimization implemented through linear programming and the second one implemented through multilayer hierarchical alternating least square nonnegative matrix factorization with sparseness constraints imposed on pure components spectra. In contrast to many existing blind decomposition methods no a priori information about the number of pure components is required. It is estimated from the mixtures using robust data clustering algorithm together with pure components concentration matrix. Proposed methodology can be implemented as a part of software packages used for the analysis of mass spectra and identification of chemical compounds.
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Affiliation(s)
- Ivica Kopriva
- Division of Laser and Atomic Research and Development, Ruder Bosković Institute, Bijenicka cesta 54, HR-10000, Zagreb, Croatia.
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25
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Kalaitzis JA, Cheng Q, Thomas PM, Kelleher NL, Moore BS. In vitro biosynthesis of unnatural enterocin and wailupemycin polyketides. JOURNAL OF NATURAL PRODUCTS 2009; 72:469-72. [PMID: 19215142 PMCID: PMC2765504 DOI: 10.1021/np800598t] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nature has evolved finely tuned strategies to synthesize rare and complex natural products such as the enterocin family of polyketides from the marine bacterium Streptomyces maritimus. Herein we report the directed ex vivo multienzyme syntheses of 24 unnatural 5-deoxyenterocin and wailupemycin F and G analogues, 18 of which are new. We have generated molecular diversity by priming the enterocin biosynthesis enzymes with unnatural substrates and have illustrated further the uniqueness of this type II polyketide synthase by way of exploiting its unusual starter unit biosynthesis pathways.
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Affiliation(s)
- John A. Kalaitzis
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, 92093-0204
| | - Qian Cheng
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, 92093-0204
| | - Paul M. Thomas
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Neil L. Kelleher
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Bradley S. Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, 92093-0204
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, 92093-0204
- Corresponding author. Tel: (858) 822-6650. Fax: (858) 558-3702. E-mail:
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