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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Dorfan Y, Nahami A, Morris Y, Shohat B, Kolodkin-Gal I. The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties. Microorganisms 2024; 12:1226. [PMID: 38930607 PMCID: PMC11205451 DOI: 10.3390/microorganisms12061226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into paint. "Mold" refers to the ubiquitous fungal species that generate visible multicellular filaments commonly found in household dust. The development of mold leads to severe health problems for occupants, including allergic response, hypersensitivity pneumonitis, and asthma, which have significant economic and clinical outcomes. We here demonstrate the robust effect of a commercial paint enhanced with Bacillus subtilis cells against the common mold agent, Aspergillus niger, and identify three biosynthetic clusters essential for this effect. Our results lay the foundation for bio-convergence and synthetic biology approaches to introduce renewable and environmentally friendly bio-anti-fungal agents into the built environment.
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Affiliation(s)
- Yuval Dorfan
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Avichay Nahami
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
- The Scojen Institute for Synthetic Biology, Reichman University, Herzliya 4610101, Israel
| | - Yael Morris
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Benny Shohat
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Ilana Kolodkin-Gal
- The Scojen Institute for Synthetic Biology, Reichman University, Herzliya 4610101, Israel
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3
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Yang Y, Yu L, Qiu X, Xiong D, Tian C. A putative terpene cyclase gene ( CcPtc1) is required for fungal development and virulence in Cytospora chrysosperma. Front Microbiol 2023; 14:1084828. [PMID: 36891381 PMCID: PMC9986285 DOI: 10.3389/fmicb.2023.1084828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Cytospora chrysosperma is a destructive plant pathogenic fungus, which causes canker disease on numerous woody plants. However, knowledge concerning the interaction between C. chrysosperma and its host remains limited. Secondary metabolites produced by phytopathogens often play important roles in their virulence. Terpene cyclases (TC), polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) are the key components for the synthesis of secondary metabolites. Here, we characterized the functions of a putative terpene type secondary metabolite biosynthetic core gene CcPtc1 in C. chrysosperma, which was significantly up-regulated in the early stages of infection. Importantly, deletion of CcPtc1 greatly reduced fungal virulence to the poplar twigs and they also showed significantly reduced fungal growth and conidiation compared with the wild-type (WT) strain. Furthermore, toxicity test of the crude extraction from each strain showed that the toxicity of crude extraction secreted by ΔCcPtc1 were strongly compromised in comparison with the WT strain. Subsequently, the untargeted metabolomics analyses between ΔCcPtc1 mutant and WT strain were conducted, which revealed 193 significantly different abundant metabolites (DAMs) inΔCcPtc1 mutant compared to the WT strain, including 90 significantly downregulated metabolites and 103 significantly up-regulated metabolites, respectively. Among them, four key metabolic pathways that reported to be important for fungal virulence were enriched, including pantothenate and coenzyme A (CoA) biosynthesis. Moreover, we also detected significant alterations in a series of terpenoids, among which (+)-ar-turmerone, pulegone, ethyl chrysanthemumate, and genipin were significantly down-regulated, while cuminaldehyde and (±)-abscisic acid were significantly up-regulated. In conclusion, our results demonstrated that CcPtc1 acts as a virulence-related secondary metabolism factor and provides new insights into the pathogenesis of C. chrysosperma.
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Affiliation(s)
- Yuchen Yang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Lu Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Xiaolin Qiu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Dianguang Xiong
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
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4
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The Rare Actinobacterium Crossiella sp. Is a Potential Source of New Bioactive Compounds with Activity against Bacteria and Fungi. Microorganisms 2022; 10:microorganisms10081575. [PMID: 36013993 PMCID: PMC9415966 DOI: 10.3390/microorganisms10081575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance has become a global problem in recent decades. A gradual reduction in drug discoveries has led to the current antimicrobial resistance crisis. Caves and other subsurface environments are underexplored thus far, and they represent indispensable ecological niches that could offer new molecules of interest to medicine and biotechnology. We explored Spanish show caves to test the bioactivity of the bacteria dwelling in the walls and ceilings, as well as airborne bacteria. We reported the isolation of two strains of the genus Crossiella, likely representing a new species, isolated from Altamira Cave, Spain. In vitro and in silico analyses showed the inhibition of pathogenic Gram-positive and Gram-negative bacteria, and fungi, as well as the taxonomical distance of both strains from their closest relative, Crossiella cryophila. The presence of an exclusive combination of gene clusters involved in the synthesis of lanthipeptides, lasso peptides, nonribosomal peptides and polyketides indicates that species of this genus could represent a source of new compounds. Overall, there is promising evidence for antimicrobial discovery in subterranean environments, which increases the possibility of identifying new bioactive molecules.
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5
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Maan H, Itkin M, Malitsky S, Friedman J, Kolodkin-Gal I. Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors. Nat Commun 2022; 13:431. [PMID: 35058430 PMCID: PMC8776889 DOI: 10.1038/s41467-021-27904-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Abstract
Microbial communities employ a variety of complex strategies to compete successfully against competitors sharing their niche, with antibiotic production being a common strategy of aggression. Here, by systematic evaluation of four non-ribosomal peptides/polyketide (NRPs/PKS) antibiotics produced by Bacillus subtilis clade, we revealed that they acted synergistically to effectively eliminate phylogenetically distinct competitors. The production of these antibiotics came with a fitness cost manifested in growth inhibition, rendering their synthesis uneconomical when growing in proximity to a phylogenetically close species, carrying resistance against the same antibiotics. To resolve this conflict and ease the fitness cost, antibiotic production was only induced by the presence of a peptidoglycan cue from a sensitive competitor, a response mediated by the global regulator of cellular competence, ComA. These results experimentally demonstrate a general ecological concept - closely related communities are favoured during competition, due to compatibility in attack and defence mechanisms.
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Affiliation(s)
- Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Maxim Itkin
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Sergey Malitsky
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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6
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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7
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Chemoenzymatic Synthesis of Starting Materials and Characterization of Halogenases Requiring Acyl Carrier Protein-Tethered Substrates. Methods Enzymol 2018; 604:333-366. [PMID: 29779658 DOI: 10.1016/bs.mie.2018.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Flavin-adenine dinucleotide (FAD)-dependent halogenases are widespread in natural product biosynthetic gene clusters and have been demonstrated to employ small organic molecules as substrates for halogenation, as well as substrates that are tethered to carrier proteins (CPs). Despite numerous reports of FAD-dependent halogenases utilizing CP-tethered substrates, only a few have been biochemically characterized due to limited accessibility to the physiological substrates. Here, we describe a method for the preparation of acyl-S-CP substrates and their use in biochemical assays to query the activity of FAD-dependent halogenases. Furthermore, we describe a mass spectrometry-based method for the characterization of acyl-S-CP substrates and the corresponding halogenated products generated by the halogenases. Finally, we test the substrate specificity of a physiological chlorinase and a physiological brominase from marine bacteria, and, for the first time, demonstrate the distinct halide specificity of halogenases. The methodology described here will enable characterization of new halogenases employing CP-tethered substrates.
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8
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Agarwal V, Diethelm S, Ray L, Garg N, Awakawa T, Dorrestein PC, Moore BS. Chemoenzymatic Synthesis of Acyl Coenzyme A Substrates Enables in Situ Labeling of Small Molecules and Proteins. Org Lett 2015; 17:4452-5. [PMID: 26333306 DOI: 10.1021/acs.orglett.5b02113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A chemoenzymatic approach to generate fully functional acyl coenzyme A molecules that are then used as substrates to drive in situ acyl transfer reactions is described. Mass spectrometry based assays to verify the identity of acyl coenzyme A enzymatic products are also illustrated. The approach is responsive to a diverse array of carboxylic acids that can be elaborated to their corresponding coenzyme A thioesters, with potential applications in wide-ranging chemical biology studies that utilize acyl coenzyme A substrates.
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Affiliation(s)
| | | | | | | | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Tokyo 113-0033, Japan
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9
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Thibodeaux C, Ha T, van der Donk WA. A price to pay for relaxed substrate specificity: a comparative kinetic analysis of the class II lanthipeptide synthetases ProcM and HalM2. J Am Chem Soc 2014; 136:17513-29. [PMID: 25409537 PMCID: PMC4277782 DOI: 10.1021/ja5089452] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Indexed: 11/28/2022]
Abstract
Lanthipeptides are a class of ribosomally synthesized and posttranslationally modified peptide natural products (RiPPs) that typically harbor multiple intramolecular thioether linkages. For class II lanthipeptides, these cross-links are installed in a multistep reaction pathway by a single enzyme (LanM). The multifunctional nature of LanMs and the manipulability of their genetically encoded peptide substrates (LanAs) make LanM/LanA systems promising targets for the engineering of new antibacterial compounds. Here, we report the development of a semiquantitative mass spectrometry-based assay for kinetic characterization of LanM-catalyzed reactions. The assay was used to conduct a comparative kinetic analysis of two LanM enzymes (HalM2 and ProcM) that exhibit drastically different substrate selectivity. Numerical simulation of the kinetic data was used to develop models for the multistep HalM2- and ProcM-catalyzed reactions. These models illustrate that HalM2 and ProcM have markedly different catalytic efficiencies for the various reactions they catalyze. HalM2, which is responsible for the biosynthesis of a single compound (the Halβ subunit of the lantibiotic haloduracin), catalyzes reactions with higher catalytic efficiency than ProcM, which modifies 29 different ProcA precursor peptides during prochlorosin biosynthesis. In particular, the rates of thioether ring formation are drastically reduced in ProcM, likely because this enzyme is charged with installing a variety of lanthipeptide ring architectures in its prochlorosin products. Thus, ProcM appears to pay a kinetic price for its relaxed substrate specificity. In addition, our kinetic models suggest that conformational sampling of the LanM/LanA Michaelis complex could play an important role in the kinetics of LanA maturation.
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Affiliation(s)
- Christopher
J. Thibodeaux
- Institute for Genomic Biology, Department of Physics, Department of Chemistry University of Illinois, Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Taekjip Ha
- Institute for Genomic Biology, Department of Physics, Department of Chemistry University of Illinois, Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Institute for Genomic Biology, Department of Physics, Department of Chemistry University of Illinois, Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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10
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Randall SM, Koryakina I, Williams GJ, Muddiman DC. Evaluating nonpolar surface area and liquid chromatography/mass spectrometry response: an application for site occupancy measurements for enzyme intermediates in polyketide biosynthesis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2511-2522. [PMID: 25366398 PMCID: PMC4230892 DOI: 10.1002/rcm.7051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/22/2014] [Accepted: 09/09/2014] [Indexed: 05/31/2023]
Abstract
RATIONALE Site occupancy measurements using liquid chromatography/mass spectrometry (LC/MS) are reported throughout the literature. However, site occupancy quantification suffers from ionization bias between modified and unmodified peptides containing the active site. In this study, we explore the MS signal as a function of nonpolar surface area (NPSA) in order to better understand this bias in electrospray response. The correlation between hydrophobicity and LC/MS response was evaluated and applied to study enzyme intermediates in polyketide synthases. METHODS Site occupancy methods were developed to study acyltransferase activity. To further evaluate these methods, several standard peptides containing one cysteine residue were modified with alkylation reagents of increasing hydrophobicity to study the MS signal as a function of NPSA. RESULTS A consistent trend in MS response was observed which is dependent on the NPSA of the analyte. An optimal NPSA zone was observed for the peptides studied. CONCLUSIONS Nonpolar surface area can be used as metric to determine relative LC/MS response for peptides and evaluate site occupancy measurements.
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Affiliation(s)
- Shan M. Randall
- W.M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Irina Koryakina
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Gavin J. Williams
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - David C. Muddiman
- W.M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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11
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de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
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12
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Agarwal V, El Gamal AA, Yamanaka K, Poth D, Kersten RD, Schorn M, Allen EE, Moore BS. Biosynthesis of polybrominated aromatic organic compounds by marine bacteria. Nat Chem Biol 2014; 10:640-7. [PMID: 24974229 PMCID: PMC4104138 DOI: 10.1038/nchembio.1564] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 05/19/2014] [Indexed: 01/06/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) and polybrominated bipyrroles are natural products that bioaccumulate in the marine food chain. PBDEs have attracted widespread attention due to their persistence in the environment and potential toxicity to humans. However, the natural origins of PBDE biosynthesis are not known. Here we report marine bacteria as producers of PBDEs and establish a genetic and molecular foundation for their production that unifies paradigms for the elaboration of bromophenols and bromopyrroles abundant in marine biota. We provide biochemical evidence of marine brominase enzymes revealing decarboxylative-halogenation enzymology previously unknown among halogenating enzymes. Biosynthetic motifs discovered in our study were used to mine sequence databases to discover unrealized marine bacterial producers of organobromine compounds.
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Affiliation(s)
- Vinayak Agarwal
- 1] Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA. [2]
| | - Abrahim A El Gamal
- 1] Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA. [2]
| | - Kazuya Yamanaka
- 1] Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA. [2]
| | - Dennis Poth
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA
| | - Roland D Kersten
- 1] Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA. [2]
| | - Michelle Schorn
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA
| | - Eric E Allen
- 1] Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA. [2] Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA. [3] Division of Biological Sciences, University of California-San Diego, La Jolla, California, USA
| | - Bradley S Moore
- 1] Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA. [2] Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California, USA. [3] Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, California, USA
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13
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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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14
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Guthals A, Watrous JD, Dorrestein PC, Bandeira N. The spectral networks paradigm in high throughput mass spectrometry. MOLECULAR BIOSYSTEMS 2013; 8:2535-44. [PMID: 22610447 DOI: 10.1039/c2mb25085c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
High-throughput proteomics is made possible by a combination of modern mass spectrometry instruments capable of generating many millions of tandem mass (MS(2)) spectra on a daily basis and the increasingly sophisticated associated software for their automated identification. Despite the growing accumulation of collections of identified spectra and the regular generation of MS(2) data from related peptides, the mainstream approach for peptide identification is still the nearly two decades old approach of matching one MS(2) spectrum at a time against a database of protein sequences. Moreover, database search tools overwhelmingly continue to require that users guess in advance a small set of 4-6 post-translational modifications that may be present in their data in order to avoid incurring substantial false positive and negative rates. The spectral networks paradigm for analysis of MS(2) spectra differs from the mainstream database search paradigm in three fundamental ways. First, spectral networks are based on matching spectra against other spectra instead of against protein sequences. Second, spectral networks find spectra from related peptides even before considering their possible identifications. Third, spectral networks determine consensus identifications from sets of spectra from related peptides instead of separately attempting to identify one spectrum at a time. Even though spectral networks algorithms are still in their infancy, they have already delivered the longest and most accurate de novo sequences to date, revealed a new route for the discovery of unexpected post-translational modifications and highly-modified peptides, enabled automated sequencing of cyclic non-ribosomal peptides with unknown amino acids and are now defining a novel approach for mapping the entire molecular output of biological systems that is suitable for analysis with tandem mass spectrometry. Here we review the current state of spectral networks algorithms and discuss possible future directions for automated interpretation of spectra from any class of molecules.
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Affiliation(s)
- Adrian Guthals
- Dept. Computer Science and Engineering, University of California, San Diego, USA
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15
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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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16
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Agarwal A, Kahyaoglu C, Hansen DB. Characterization of HmqF, a Protein Involved in the Biosynthesis of Unsaturated Quinolones Produced by Burkholderia thailandensis. Biochemistry 2012; 51:1648-57. [DOI: 10.1021/bi201625w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Aparna Agarwal
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey
07102, United States
| | - Caroline Kahyaoglu
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey
07102, United States
| | - Darren B. Hansen
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey
07102, United States
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17
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Bonnett SA, Rath CM, Shareef AR, Joels JR, Chemler JA, Håkansson K, Reynolds K, Sherman DH. Acyl-CoA subunit selectivity in the pikromycin polyketide synthase PikAIV: steady-state kinetics and active-site occupancy analysis by FTICR-MS. ACTA ACUST UNITED AC 2012; 18:1075-81. [PMID: 21944746 DOI: 10.1016/j.chembiol.2011.07.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 06/23/2011] [Accepted: 07/04/2011] [Indexed: 10/17/2022]
Abstract
Polyketide natural products generated by type I modular polyketide synthases (PKSs) are vital components in our drug repertoire. To reprogram these biosynthetic assembly lines, we must first understand the steps that occur within the modular "black boxes." Herein, key steps of acyl-CoA extender unit selection are explored by in vitro biochemical analysis of the PikAIV PKS model system. Two complementary approaches are employed: a fluorescent-probe assay for steady-state kinetic analysis, and Fourier Transform Ion Cyclotron Resonance-mass spectrometry (FTICR-MS) to monitor active-site occupancy. Findings from five enzyme variants and four model substrates have enabled a model to be proposed involving catalysis based upon acyl-CoA substrate loading followed by differential rates of hydrolysis. These efforts suggest a strategy for future pathway engineering efforts using unnatural extender units with slow rates of hydrolytic off-loading from the acyltransferase domain.
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Affiliation(s)
- Shilah A Bonnett
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
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18
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Analysis of the ketosynthase-chain length factor heterodimer from the fredericamycin polyketide synthase. ACTA ACUST UNITED AC 2011; 18:1021-31. [PMID: 21867917 DOI: 10.1016/j.chembiol.2011.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 05/01/2011] [Accepted: 05/03/2011] [Indexed: 11/24/2022]
Abstract
The pentadecaketide fredericamycin has the longest carbon chain backbone among polycyclic aromatic polyketide antibiotics whose biosynthetic genes have been sequenced. This backbone is synthesized by the bimodular fdm polyketide synthase (PKS). Here, we demonstrate that the bimodular fdm PKS as well as its elongation module alone synthesize undecaketides and dodecaketides. Thus, unlike other homologs, the fdm ketosynthase-chain length factor (KS-CLF) heterodimer does not exclusively control the backbone length of its natural product. Using sequence- and structure-based approaches, 48 CLF multiple mutants were engineered and analyzed. Unexpectedly, the I134F mutant was unable to turn over but could initiate and partially elongate the polyketide chain. This unprecedented mutant suggests that the KS-CLF heterodimer harbors an as yet uncharacterized chain termination mechanism. Together, our findings reveal fundamental mechanistic differences between the fdm PKS and its well-studied homologs.
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19
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Ding Y, Rath CM, Bolduc KL, Håkansson K, Sherman DH. Chemoenzymatic synthesis of cryptophycin anticancer agents by an ester bond-forming non-ribosomal peptide synthetase module. J Am Chem Soc 2011; 133:14492-5. [PMID: 21823639 DOI: 10.1021/ja204716f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cryptophycins (Crp) are a group of cyanobacterial depsipeptides with activity against drug-resistant tumors. Although they have been shown to be promising, further efforts are required to return these highly potent compounds to the clinic through a new generation of analogues with improved medicinal properties. Herein, we report a chemosynthetic route relying on the multifunctional enzyme CrpD-M2 that incorporates a 2-hydroxy acid moiety (unit D) into Crp analogues. CrpD-M2 is a unique non-ribosomal peptide synthetase (NRPS) module comprised of condensation-adenylation-ketoreduction-thiolation (C-A-KR-T) domains. We interrogated A-domain 2-keto and 2-hydroxy acid activation and loading, and KR domain activity in the presence of NADPH and NADH. The resulting 2-hydroxy acid was elongated with three synthetic Crp chain elongation intermediate analogues through ester bond formation catalyzed by CrpD-M2 C domain. Finally, the enzyme-bound seco-Crp products were macrolactonized by the Crp thioesterase. Analysis of these sequential steps was enabled through LC-FTICR-MS of enzyme-bound intermediates and products. This novel chemoenzymatic synthesis of Crp involves four sequential catalytic steps leading to the incorporation of a 2-hydroxy acid moiety in the final chain elongation intermediate. The presented work constitutes the first example where a NRPS-embedded KR domain is employed for assembly of a fully elaborated natural product, and serves as a proof-of-principle for chemoenzymatic synthesis of new Crp analogues.
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Affiliation(s)
- Yousong Ding
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
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20
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Mann S, Lombard B, Loew D, Méjean A, Ploux O. Insights into the Reaction Mechanism of the Prolyl–Acyl Carrier Protein Oxidase Involved in Anatoxin-a and Homoanatoxin-a Biosynthesis. Biochemistry 2011; 50:7184-97. [DOI: 10.1021/bi200892a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stéphane Mann
- Laboratoire
Charles Friedel,
Chimie ParisTech, ENSCP, 11 rue Pierre
et Marie Curie, 75231 Paris Cedex 05, France
- CNRS, UMR 7223, 75005
Paris, France
| | - Bérangère Lombard
- Laboratory of Proteomic Mass
Spectrometry, Centre de Recherche, Institut Curie, 26 rue d'Ulm 75248, Paris Cedex 05, France
| | - Damarys Loew
- Laboratory of Proteomic Mass
Spectrometry, Centre de Recherche, Institut Curie, 26 rue d'Ulm 75248, Paris Cedex 05, France
| | - Annick Méjean
- Laboratoire
Charles Friedel,
Chimie ParisTech, ENSCP, 11 rue Pierre
et Marie Curie, 75231 Paris Cedex 05, France
- CNRS, UMR 7223, 75005
Paris, France
- Université Paris Diderot-Paris 7, 75013 Paris, France
| | - Olivier Ploux
- Laboratoire
Charles Friedel,
Chimie ParisTech, ENSCP, 11 rue Pierre
et Marie Curie, 75231 Paris Cedex 05, France
- CNRS, UMR 7223, 75005
Paris, France
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21
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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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22
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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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23
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Meier JL, Patel AD, Niessen S, Meehan M, Kersten R, Yang JY, Rothmann M, Cravatt BF, Dorrestein PC, Burkart MD, Bafna V. Practical 4'-phosphopantetheine active site discovery from proteomic samples. J Proteome Res 2010; 10:320-9. [PMID: 21067235 DOI: 10.1021/pr100953b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Polyketide and nonribosomal peptides constitute important classes of small molecule natural products. Due to the proven biological activities of these compounds, novel methods for discovery and study of the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymes responsible for their production remains an area of intense interest, and proteomic approaches represent a relatively unexplored avenue. While these enzymes may be distinguished from the proteomic milieu by their use of the 4'-phosphopantetheine (PPant) post-translational modification, proteomic detection of PPant peptides is hindered by their low abundance and labile nature which leaves them unassigned using traditional database searching. Here we address key experimental and computational challenges to facilitate practical discovery of this important post-translational modification during shotgun proteomics analysis using low-resolution ion-trap mass spectrometers. Activity-based enrichment maximizes MS input of PKS/NRPS peptides, while targeted fragmentation detects putative PPant active sites. An improved data analysis pipeline allows experimental identification and validation of these PPant peptides directly from MS² data. Finally, a machine learning approach is developed to directly detect PPant peptides from only MS² fragmentation data. By providing new methods for analysis of an often cryptic post-translational modification, these methods represent a first step toward the study of natural product biosynthesis in proteomic settings.
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Affiliation(s)
- Jordan L Meier
- Department of Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla California 92093, USA
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24
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Zhou H, Qiao K, Gao Z, Meehan MJ, Li JWH, Zhao X, Dorrestein PC, Vederas JC, Tang Y. Enzymatic synthesis of resorcylic acid lactones by cooperation of fungal iterative polyketide synthases involved in hypothemycin biosynthesis. J Am Chem Soc 2010; 132:4530-1. [PMID: 20222707 PMCID: PMC2861853 DOI: 10.1021/ja100060k] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hypothemycin is a macrolide protein kinase inhibitor from the fungus Hypomyces subiculosus. During biosynthesis, its carbon framework is assembled by two iterative polyketide synthases (PKSs), Hpm8 (highly reducing) and Hpm3 (nonreducing). These were heterologously expressed in Saccharomyces cerevisiae BJ5464-NpgA, purified to near homogeneity, and reconstituted in vitro to produce (6'S,10'S)-trans-7',8'-dehydrozearalenol (1) from malonyl-CoA and NADPH. The structure of 1 was determined by X-ray crystallographic analysis. In the absence of functional Hpm3, the reducing PKS Hpm8 produces and offloads truncated pyrone products instead of the expected hexaketide. The nonreducing Hpm3 is able to accept an N-acetylcysteamine thioester of a correctly functionalized hexaketide to form 1, but it is unable to initiate polyketide formation from malonyl-CoA. We show that the starter-unit:ACP transacylase (SAT) of Hpm3 is critical for crosstalk between the two enzymes and that the rate of biosynthesis of 1 is determined by the rate of hexaketide formation by Hpm8.
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Affiliation(s)
- Hui Zhou
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
| | - Kangjian Qiao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
| | - Zhizeng Gao
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Michael J. Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Departments of Pharmacology, Chemistry and Biochemistry, University of California, San Diego, CA 92093
| | - Jesse W.-H. Li
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Xiling Zhao
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Departments of Pharmacology, Chemistry and Biochemistry, University of California, San Diego, CA 92093
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Departments of Pharmacology, Chemistry and Biochemistry, University of California, San Diego, CA 92093
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
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25
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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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26
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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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27
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A proteomics approach to discovering natural products and their biosynthetic pathways. Nat Biotechnol 2009; 27:951-6. [PMID: 19767731 PMCID: PMC2782881 DOI: 10.1038/nbt.1565] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 08/31/2009] [Indexed: 11/08/2022]
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28
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Xie X, Meehan MJ, Xu W, Dorrestein PC, Tang Y. Acyltransferase mediated polyketide release from a fungal megasynthase. J Am Chem Soc 2009; 131:8388-9. [PMID: 19530726 DOI: 10.1021/ja903203g] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LovF is a highly reducing polyketide synthase (HR-PKS) from the filamentous fungus Aspergillus terreus. LovF synthesizes the alpha-S-methylbutyrate side chain that is subsequently transferred to monacolin J to yield the cholesterol-lowering natural product lovastatin. In the report, we expressed the full length LovF and reconstituted the megasynthase activities in vitro. We confirmed the diketide product of LovF is offloaded from the LovF ACP domain by the dissociated acyltransferase LovD. This represents the first example of acyltransferase-mediated release of polyketide products from fungal PKSs. We determined LovD primarily interacts with the ACP domain of LovF and the protein-protein interactions lead to highly efficient transfer of the diketide product. The catalytic efficiency is enhanced nearly 1 x 10(6)-fold when LovF was used as the acyl carrier instead of N-acetylcysteamine. Reconstitution and characterization of the LovF offloading mechanism provide new insights into the functions of fungal HR-PKS.
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Affiliation(s)
- Xinkai Xie
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, USA
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29
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Vater J, Wilde C, Kell H. In situ detection of the intermediates in the biosynthesis of surfactin, a lipoheptapeptide from Bacillus subtilis OKB 105, by whole-cell cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in combination with mutant analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:1493-1498. [PMID: 19350532 DOI: 10.1002/rcm.4031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An innovative technique to investigate the intermediates involved in the biosynthesis of the lipoheptapeptide surfactin from Bacillus subtilis OKB105 combining whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) with targeted generation of knock-out mutants was demonstrated. This method allows efficient, sensitive detection of biosynthetic intermediates in a minimum of time directly at the outer surface of microbial cells picked from agar plates or in surface extracts prepared thereof. Biosynthesis of surfactin is encoded by the srf-operon which is organized into four open reading frames which have been attributed to three multifunctional NRPS enzymes (SrfA-C) and a thioesterase/acyltransferase enzyme SrfD. For the wild-type strain OKB 105 only the end product surfactin was found mass spectrometrically. For the detection of lipopeptide intermediates three plasmid- and transposon-insertion mutants were generated interrupting the surfactin assembly line at defined positions. Strain LAB 327 was mutated in the spacer region between enzymes SrfA and B. Here only SrfA was active with the lipotripeptide beta-OH-acyl-L-Glu-L-Leu-D-Leu as the end product. Mutant OKB 120 bears a transposon mutation in SrfB between the first and second amino acid activating modules SrfB1 and SrfB2. It showed all intermediates from the lipodi- until to the lipotetrapeptide beta-OH-acyl-L-Glu-L-Leu-D-Leu-L-Val. In LAB 223 SrfC was knocked out by a transposon mutation. It produced the lipohexapeptide beta-OH-acyl-L-Glu-L-Leu-D-Leu-L-Val-L-Asp-D-Leu. Our work highlights the applicability and the potential of whole-cell MALDI-TOFMS as an innovative efficient tool for the analysis of intermediate steps of biosynthetic pathways.
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Affiliation(s)
- Joachim Vater
- Institut für Chemie, Arbeitsgruppe Biochemie und Molekulare Biologie, Technische Universität Berlin, Franklinstr. 29, D-10587 Berlin, Germany.
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30
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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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31
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Bumpus SB, Kelleher NL. Accessing natural product biosynthetic processes by mass spectrometry. Curr Opin Chem Biol 2009; 12:475-82. [PMID: 18706516 DOI: 10.1016/j.cbpa.2008.07.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 06/23/2008] [Accepted: 07/17/2008] [Indexed: 11/16/2022]
Abstract
Two important classes of natural products are made by nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). With most biosynthetic intermediates covalently tethered during biogenesis, protein mass spectrometry (MS) has proven invaluable for their interrogation. New mass spectrometric assay formats (such as selective cofactor ejection and proteomics style LC-MS) are showcased here in the context of functional insights into new breeds of NRPS/PKS enzymes, including the first characterization of an 'iterative' PKS, the biosynthesis of the enediyne antitumor antibiotics, the study of a new strategy for PKS initiation via a GNAT-like mechanism, and the analysis of branching strategies in the so-called 'AT-less' NRPS/PKS hybrid systems. The future of MS analysis of NRPS and PKS biosynthetic pathways lies in adoption and development of methods that continue bridging enzymology with proteomics as both fields continue their post-genomic acceleration.
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Affiliation(s)
- Stefanie B Bumpus
- Department of Chemistry & The Institute for Genomic Biology, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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32
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Burns KE, Liu WT, Boshoff HIM, Dorrestein PC, Barry CE. Proteasomal protein degradation in Mycobacteria is dependent upon a prokaryotic ubiquitin-like protein. J Biol Chem 2009; 284:3069-3075. [PMID: 19028679 PMCID: PMC2631945 DOI: 10.1074/jbc.m808032200] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 11/17/2008] [Indexed: 01/27/2023] Open
Abstract
The striking identification of an apparent proteasome core in Mycobacteria and allied actinomycetes suggested that additional elements of this otherwise strictly eukaryotic system for regulated protein degradation might be conserved. The genes encoding this prokaryotic proteasome are clustered in an operon with a short open reading frame that encodes a small protein of 64 amino acids resembling ubiquitin with a carboxyl-terminal di-glycine-glutamine motif (herein called Pup for prokaryotic ubiquitin-like protein). Expression of a polyhistidine-tagged Pup followed by pulldown revealed that a broad spectrum of proteins were post-translationally modified by Pup. Two-dimensional gel electrophoresis allowed us to conclusively identify two targets of this modification as myoinositol-1-phosphate synthase and superoxide dismutase. Deletion of the penultimate di-glycine motif or the terminal glutamine completely abrogated modification of cellular proteins with Pup. Further mass spectral analysis demonstrated that Pup was attached to a lysine residue on its target protein via the carboxyl-terminal glutamine with deamidation of this residue. Finally, we showed that cell lysates of wild type (but not a proteasome mutant) efficiently degraded Pup-modified proteins. These data therefore establish that, despite differences in both sequence and target linkage, Pup plays an analogous role to ubiquitin in targeting proteins to the proteasome for degradation.
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Affiliation(s)
- Kristin E Burns
- Tuberculosis Research Section, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Wei-Ting Liu
- Departments of Pharmacology, Chemistry, and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093
| | - Helena I M Boshoff
- Tuberculosis Research Section, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Pieter C Dorrestein
- Departments of Pharmacology, Chemistry, and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093
| | - Clifton E Barry
- Tuberculosis Research Section, NIAID, National Institutes of Health, Bethesda, Maryland 20892.
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33
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Meier JL, Burkart MD. The chemical biology of modular biosynthetic enzymes. Chem Soc Rev 2009; 38:2012-45. [DOI: 10.1039/b805115c] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Chapter 9. Synthetic probes for polyketide and nonribosomal peptide biosynthetic enzymes. Methods Enzymol 2009; 458:219-54. [PMID: 19374985 DOI: 10.1016/s0076-6879(09)04809-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Polyketides and nonribosomal peptides constitute two classes of small molecule natural products that are well-known for their ability to impact important biological processes in a multitude of ways. The modular biosynthetic enzymes responsible for production of these compounds (PKS and NRPS enzymes) have been the subject of extensive genetic, biochemical, and structural characterization, in part due to the potential utility their successful reengineering may have for the production of new therapeutics. In this chapter, we provide background as well as specific techniques in which synthetically produced small molecule probes have been applied to help better understand the mechanism and structure of PKS and NRPS biosynthetic pathways, as well as to help streamline their discovery process. The continued development and application of these methods has the potential to greatly complement our current approaches to the study of natural product biosynthesis.
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Bumpus SB, Magarvey NA, Kelleher NL, Walsh CT, Calderone CT. Polyunsaturated fatty-acid-like trans-enoyl reductases utilized in polyketide biosynthesis. J Am Chem Soc 2008; 130:11614-6. [PMID: 18693732 PMCID: PMC2627581 DOI: 10.1021/ja8040042] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyketide biosynthesis is typically directed by cis-acting catalytic domains. In the case of the Bacillus subtilis secondary metabolite dihydrobacillaene, the cis-acting domains are not sufficient to generate the saturated C14'-C15' bond. In this communication, we identify PksE as a trans-acting enoyl reductase utilized in the biosynthesis of this portion of dihydrobacillaene. PksE is homologous to the enzymes predicted to serve as enoyl reductases in polyunsaturated fatty acid (PUFA) biosynthesis, and we confirmed this functional assignment in vitro. These results suggest a general enoyl reduction pathway in polyketide biosynthesis and a means by which PUFA-like biosynthetic machinery can modulate small-molecule function.
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Affiliation(s)
- Stefanie B. Bumpus
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Nathan A. Magarvey
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115
| | - Neil L. Kelleher
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Christopher T. Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115
| | - Christopher T. Calderone
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115
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37
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Peering inside the black box to find enzyme-bound intermediates. Nat Chem Biol 2008; 4:390-1. [DOI: 10.1038/nchembio0708-390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Meier JL, Mercer AC, Burkart MD. Fluorescent Profiling of Modular Biosynthetic Enzymes by Complementary Metabolic and Activity Based Probes. J Am Chem Soc 2008; 130:5443-5. [DOI: 10.1021/ja711263w] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jordan L. Meier
- Department of Chemistry and Biochemistry, University of California—San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358
| | - Andrew C. Mercer
- Department of Chemistry and Biochemistry, University of California—San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California—San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358
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39
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Kopp F, Linne U, Oberthür M, Marahiel MA. Harnessing the chemical activation inherent to carrier protein-bound thioesters for the characterization of lipopeptide fatty acid tailoring enzymes. J Am Chem Soc 2008; 130:2656-66. [PMID: 18237171 DOI: 10.1021/ja078081n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Here, we report a new experimental approach utilizing an amide ligation reaction for the characterization of acyl carrier protein (ACP)-bound reaction intermediates, which are otherwise difficult to analyze by traditional biochemical methods. To explore fatty acid tailoring enzymes of the calcium-dependent antibiotic (CDA) biosynthetic pathway, this strategy enabled the transformation of modified fatty acids, covalently bound as thioesters to an ACP, into amide ligation products that can be directly analyzed and compared to synthetic standards by HPLC-MS. The driving force of the amide formation is the thermodynamic activation inherent to thioester-bound compounds. Using this novel method, we were able to characterize the ACP-mediated biosynthesis of the unique 2,3-epoxyhexanoyl moiety of CDA, revealing a new type of FAD-dependent oxidase HxcO with intrinsic enoyl-ACP epoxidase activity, as well as a second enoyl-ACP epoxidase, HcmO. In general, our approach should be widely applicable for the in vitro characterization of other biosynthetic systems acting on carrier proteins, such as integrated enzymes from NRPS and PKS assembly lines or tailoring enzymes of fatty and amino acid precursor synthesis.
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Affiliation(s)
- Florian Kopp
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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40
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A phosphopantetheinylating polyketide synthase producing a linear polyene to initiate enediyne antitumor antibiotic biosynthesis. Proc Natl Acad Sci U S A 2008; 105:1460-5. [PMID: 18223152 DOI: 10.1073/pnas.0711625105] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enediynes, unified by their unique molecular architecture and mode of action, represent some of the most potent anticancer drugs ever discovered. The biosynthesis of the enediyne core has been predicted to be initiated by a polyketide synthase (PKS) that is distinct from all known PKSs. Characterization of the enediyne PKS involved in C-1027 (SgcE) and neocarzinostatin (NcsE) biosynthesis has now revealed that (i) the PKSs contain a central acyl carrier protein domain and C-terminal phosphopantetheinyl transferase domain; (ii) the PKSs are functional in heterologous hosts, and coexpression with an enediyne thioesterase gene produces the first isolable compound, 1,3,5,7,9,11,13-pentadecaheptaene, in enediyne core biosynthesis; and (iii) the findings for SgcE and NcsE are likely shared among all nine-membered enediynes, thereby supporting a common mechanism to initiate enediyne biosynthesis.
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41
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Tocilj A, Munger C, Proteau A, Morona R, Purins L, Ajamian E, Wagner J, Papadopoulos M, Van Den Bosch L, Rubinstein JL, Féthière J, Matte A, Cygler M. Bacterial polysaccharide co-polymerases share a common framework for control of polymer length. Nat Struct Mol Biol 2008; 15:130-8. [PMID: 18204465 DOI: 10.1038/nsmb.1374] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 12/07/2007] [Indexed: 11/09/2022]
Abstract
The chain length distribution of complex polysaccharides present on the bacterial surface is determined by polysaccharide co-polymerases (PCPs) anchored in the inner membrane. We report crystal structures of the periplasmic domains of three PCPs that impart substantially different chain length distributions to surface polysaccharides. Despite very low sequence similarities, they have a common protomer structure with a long central alpha-helix extending 100 A into the periplasm. The protomers self-assemble into bell-shaped oligomers of variable sizes, with a large internal cavity. Electron microscopy shows that one of the full-length PCPs has a similar organization as that observed in the crystal for its periplasmic domain alone. Functional studies suggest that the top of the PCP oligomers is an important region for determining polysaccharide modal length. These structures provide a detailed view of components of the bacterial polysaccharide assembly machinery.
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Affiliation(s)
- Ante Tocilj
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montréal, Québec H3G 1Y6, Canada
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42
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Sattely ES, Fischbach MA, Walsh CT. Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways. Nat Prod Rep 2008; 25:757-93. [DOI: 10.1039/b801747f] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Feng X, Siegel MM. FTICR-MS applications for the structure determination of natural products. Anal Bioanal Chem 2007; 389:1341-63. [PMID: 17701030 DOI: 10.1007/s00216-007-1468-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Revised: 06/20/2007] [Accepted: 06/22/2007] [Indexed: 10/23/2022]
Abstract
Natural products are a source of unique chemical entities with specific biological activities of great value to the pharmaceutical industry. However, the determination of unknown structures is usually time consuming and often becomes a bottleneck in the effort to develop natural products into effective drugs. The high-performance features of high magnetic field FTMS have greatly alleviated the structural elucidation bottleneck to meet increasingly shorter discovery timelines for drug candidates based on natural products. The high-performance features of high field FTMS include unsurpassed mass measurement accuracy for elemental formula determination, ultra-high mass resolution for component separation, the ability to perform multiple levels of tandem mass spectrometry for structural elucidation, and moderate sensitivity for limited supply of isolates. A number of applications utilizing these properties of FTMS have been reported recently for the structural elucidation of novel natural product structures originating from terrestrial and marine microorganisms. In this review, FTMS methods and their applications for the structural elucidation and characterization of natural products will be reviewed.
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Affiliation(s)
- Xidong Feng
- Chemical and Screening Sciences, Wyeth Research, Pearl River, NY 10965, USA.
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Roongsawang N, Washio K, Morikawa M. In vivo characterization of tandem C-terminal thioesterase domains in arthrofactin synthetase. Chembiochem 2007; 8:501-12. [PMID: 17328008 DOI: 10.1002/cbic.200600465] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Macrocyclization of a peptide or a lipopeptide occurs at the last step of synthesis and is usually catalyzed by a single C-terminal thioesterase (Te) domain. Arthrofactin synthetase (Arf) from Pseudomonas sp. MIS38 represents a novel type of nonribosomal peptide synthetase that contains unique tandem C-terminal Te domains, ArfC_Te1 and ArfC_Te2. In order to analyze their function in vivo, site-directed mutagenesis was introduced at the putative active-site residues in ArfC_Te1 and ArfC_Te2. It was found that both Te domains were functional. Peaks corresponding to arthrofactin and its derivatives were absent in ArfC_Te1:S89A, ArfC_Te1:S89T, and ArfC_Te1:E26G/F27A mutants, and the production of arthrofactin by ArfC_Te2:S92A, ArfC_Te2:S92A/D118A, and ArfCDeltaTe2 was reduced by 95 % without an alteration of the cyclic lipoundecapeptide structure. These results suggest that Ser89 in ArfC_Te1 is essential for the completion of macrocyclization and the release of product. Glu26 and Phe27 residues are also part of the active site of ArfC_Te1. ArfC_Te2 might have been added during the evolution of Arf in order to improve macrocyclization efficiency.
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Affiliation(s)
- Niran Roongsawang
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
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45
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Menzella HG, Reeves CD. Combinatorial biosynthesis for drug development. Curr Opin Microbiol 2007; 10:238-45. [PMID: 17553731 DOI: 10.1016/j.mib.2007.05.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Revised: 04/09/2007] [Accepted: 05/17/2007] [Indexed: 11/17/2022]
Abstract
Combinatorial biosynthesis can refer to any strategy for the genetic engineering of natural product biosynthesis to obtain new molecules, including the use of genetics for medicinal chemistry. However, it also implies the possibility that large libraries of complex compounds might be produced to feed a modern high-throughput screening operation. This review focuses on the multi-modular enzymes that produce polyketides, nonribosomal peptides, and hybrid polyketide-peptide compounds, which are the enzymes that appear to be most amenable to truly combinatorial approaches. The recent establishment of a high-throughput strategy for testing the activity of many non-natural combinations of modules from these enzymes should help speed the advance of this technology.
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Affiliation(s)
- Hugo G Menzella
- Kosan Biosciences, Inc. 3832 Bay Center Place, Hayward, CA 94545, USA
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46
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Dorrestein PC, Bumpus SB, Calderone CT, Garneau-Tsodikova S, Aron ZD, Straight PD, Kolter R, Walsh CT, Kelleher NL. Facile detection of acyl and peptidyl intermediates on thiotemplate carrier domains via phosphopantetheinyl elimination reactions during tandem mass spectrometry. Biochemistry 2006; 45:12756-66. [PMID: 17042494 PMCID: PMC2518290 DOI: 10.1021/bi061169d] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With the emergence of drug resistance and the genomic revolution, there has been a renewed interest in the genes that are responsible for the generation of bioactive natural products. Secondary metabolites of one major class are biosynthesized at one or more sites by ultralarge enzymes that carry covalent intermediates on phosphopantetheine arms. Because such intermediates are difficult to characterize in vitro, we have developed a new approach for streamlined detection of substrates, intermediates, and products attached to a phosphopantetheinyl arm of the carrier site. During vibrational activation of gas-phase carrier domains, facile elimination occurs in benchtop and Fourier-transform mass spectrometers alike. Phosphopantetheinyl ejections quickly reduce >100 kDa megaenzymes to <1000 Da ions for structural assignment of intermediates at <0.007 Da mass accuracy without proteolytic digestion. This "top down" approach quickly illuminated diverse acyl intermediates on the carrier domains of the nonribosomal peptide synthetases (NRPSs) or polyketide synthases (PKSs) found in the biosynthetic pathways of prodigiosin, pyoluteorin, mycosubtilin, nikkomycin, enterobactin, gramicidin, and several proteins from the orphan pksX gene cluster from Bacillus subtilis. By focusing on just those regions undergoing covalent chemistry, the method delivered clean proof for the reversible dehydration of hydroxymethylglutaryl-S-PksL via incorporation of 2H or 18O from the buffer. The facile nature of this revised assay will allow diverse laboratories to spearhead their NRPS-PKS projects with benchtop mass spectrometers.
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Affiliation(s)
- Pieter C. Dorrestein
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 600 S. Mathews Ave. 61801
| | - Stefanie B. Bumpus
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 600 S. Mathews Ave. 61801
| | - Christopher T. Calderone
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Sylvie Garneau-Tsodikova
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Zachary D. Aron
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Paul D. Straight
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
| | - Roberto Kolter
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
| | - Christopher T. Walsh
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Neil L. Kelleher
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 600 S. Mathews Ave. 61801
- Corresponding author: , Fax 217−244−8068, Phone 217−244−3927. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 600 S. Mathews Ave. 61801
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